Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 04:40:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/08_2023/6utg_20878.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.114 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 238 5.16 5 C 36771 2.51 5 N 9926 2.21 5 O 11214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 58149 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "P" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "Q" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "R" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "S" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "U" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "b" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "c" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "d" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "e" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "f" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "g" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Time building chain proxies: 20.24, per 1000 atoms: 0.35 Number of scatterers: 58149 At special positions: 0 Unit cell: (132.038, 132.038, 238.162, 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 238 16.00 O 11214 8.00 N 9926 7.00 C 36771 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: 16.24 Conformation dependent library (CDL) restraints added in 6.6 seconds 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13874 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 63 sheets defined 48.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 1 142 " --> pdb=" O LEU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 Processing helix chain '1' and resid 188 through 199 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 2 142 " --> pdb=" O LEU 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 165 Processing helix chain '2' and resid 188 through 199 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.633A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.215A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.808A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.191A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.720A pdb=" N VAL C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.163A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.856A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 4.159A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.744A pdb=" N VAL E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 4.151A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.739A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.174A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.833A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.171A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'H' and resid 188 through 199 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 Processing helix chain 'I' and resid 188 through 199 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 165 Processing helix chain 'J' and resid 188 through 199 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 165 Processing helix chain 'K' and resid 188 through 199 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 165 Processing helix chain 'L' and resid 188 through 199 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 188 through 199 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR N 142 " --> pdb=" O LEU N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 165 Processing helix chain 'N' and resid 188 through 199 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER O 21 " --> pdb=" O THR O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN O 52 " --> pdb=" O GLY O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 61 Processing helix chain 'O' and resid 64 through 94 Processing helix chain 'O' and resid 104 through 122 removed outlier: 3.576A pdb=" N ILE O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 221 removed outlier: 3.666A pdb=" N LEU O 180 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG O 184 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS O 217 " --> pdb=" O LEU O 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 16 Processing helix chain 'P' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER P 21 " --> pdb=" O THR P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 52 removed outlier: 3.731A pdb=" N ASN P 52 " --> pdb=" O GLY P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 64 through 94 Processing helix chain 'P' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL P 155 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG P 184 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS P 217 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 16 Processing helix chain 'Q' and resid 17 through 31 removed outlier: 4.082A pdb=" N SER Q 21 " --> pdb=" O THR Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN Q 52 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 64 through 94 Processing helix chain 'Q' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU Q 180 " --> pdb=" O SER Q 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS Q 217 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 Processing helix chain 'R' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 61 Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 221 removed outlier: 3.666A pdb=" N LEU R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS R 217 " --> pdb=" O LEU R 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER S 21 " --> pdb=" O THR S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN S 52 " --> pdb=" O GLY S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 61 Processing helix chain 'S' and resid 64 through 94 Processing helix chain 'S' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE S 116 " --> pdb=" O ALA S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU S 180 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG S 184 " --> pdb=" O LEU S 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS S 218 " --> pdb=" O LEU S 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 16 Processing helix chain 'T' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER T 21 " --> pdb=" O THR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN T 52 " --> pdb=" O GLY T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 61 Processing helix chain 'T' and resid 64 through 94 Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.576A pdb=" N ILE T 116 " --> pdb=" O ALA T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL T 155 " --> pdb=" O ALA T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG T 184 " --> pdb=" O LEU T 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS T 218 " --> pdb=" O LEU T 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 16 Processing helix chain 'U' and resid 17 through 31 removed outlier: 4.082A pdb=" N SER U 21 " --> pdb=" O THR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN U 52 " --> pdb=" O GLY U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 61 Processing helix chain 'U' and resid 64 through 94 Processing helix chain 'U' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE U 116 " --> pdb=" O ALA U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 161 removed outlier: 3.790A pdb=" N VAL U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU U 180 " --> pdb=" O SER U 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG U 184 " --> pdb=" O LEU U 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS U 217 " --> pdb=" O LEU U 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS U 218 " --> pdb=" O LEU U 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 165 Processing helix chain 'V' and resid 188 through 199 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 Processing helix chain 'W' and resid 188 through 199 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 165 Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 165 Processing helix chain 'Y' and resid 188 through 199 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR Z 142 " --> pdb=" O LEU Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 165 Processing helix chain 'Z' and resid 188 through 199 Processing helix chain 'a' and resid 21 through 33 Processing helix chain 'a' and resid 81 through 104 Processing helix chain 'a' and resid 108 through 126 removed outlier: 3.739A pdb=" N LEU a 112 " --> pdb=" O ASN a 108 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR a 123 " --> pdb=" O GLN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 180 Processing helix chain 'a' and resid 185 through 202 removed outlier: 3.535A pdb=" N SER a 200 " --> pdb=" O ALA a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL a 229 " --> pdb=" O ASP a 225 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS a 230 " --> pdb=" O GLN a 226 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS a 231 " --> pdb=" O GLU a 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE a 232 " --> pdb=" O GLU a 228 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 33 Processing helix chain 'b' and resid 81 through 104 Processing helix chain 'b' and resid 108 through 126 removed outlier: 3.737A pdb=" N LEU b 112 " --> pdb=" O ASN b 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 185 through 202 removed outlier: 3.533A pdb=" N SER b 200 " --> pdb=" O ALA b 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 225 through 233 removed outlier: 3.704A pdb=" N VAL b 229 " --> pdb=" O ASP b 225 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS b 230 " --> pdb=" O GLN b 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS b 231 " --> pdb=" O GLU b 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE b 232 " --> pdb=" O GLU b 228 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 33 Processing helix chain 'c' and resid 81 through 104 Processing helix chain 'c' and resid 108 through 126 removed outlier: 3.744A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR c 123 " --> pdb=" O GLN c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 180 Processing helix chain 'c' and resid 185 through 202 removed outlier: 3.537A pdb=" N SER c 200 " --> pdb=" O ALA c 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 233 removed outlier: 3.702A pdb=" N VAL c 229 " --> pdb=" O ASP c 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS c 230 " --> pdb=" O GLN c 226 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE c 232 " --> pdb=" O GLU c 228 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 33 Processing helix chain 'd' and resid 81 through 104 Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.737A pdb=" N LEU d 112 " --> pdb=" O ASN d 108 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 180 Processing helix chain 'd' and resid 185 through 202 removed outlier: 3.531A pdb=" N SER d 200 " --> pdb=" O ALA d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 225 through 233 removed outlier: 3.695A pdb=" N VAL d 229 " --> pdb=" O ASP d 225 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS d 230 " --> pdb=" O GLN d 226 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS d 231 " --> pdb=" O GLU d 227 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 33 Processing helix chain 'e' and resid 81 through 104 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.742A pdb=" N LEU e 112 " --> pdb=" O ASN e 108 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR e 123 " --> pdb=" O GLN e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 180 Processing helix chain 'e' and resid 185 through 202 removed outlier: 3.531A pdb=" N SER e 200 " --> pdb=" O ALA e 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 225 through 233 removed outlier: 3.694A pdb=" N VAL e 229 " --> pdb=" O ASP e 225 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS e 230 " --> pdb=" O GLN e 226 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS e 231 " --> pdb=" O GLU e 227 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE e 232 " --> pdb=" O GLU e 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 33 Processing helix chain 'f' and resid 81 through 104 Processing helix chain 'f' and resid 108 through 126 removed outlier: 3.741A pdb=" N LEU f 112 " --> pdb=" O ASN f 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR f 123 " --> pdb=" O GLN f 119 " (cutoff:3.500A) Processing helix chain 'f' and resid 169 through 180 Processing helix chain 'f' and resid 185 through 202 removed outlier: 3.538A pdb=" N SER f 200 " --> pdb=" O ALA f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 233 removed outlier: 3.697A pdb=" N VAL f 229 " --> pdb=" O ASP f 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS f 230 " --> pdb=" O GLN f 226 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS f 231 " --> pdb=" O GLU f 227 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE f 232 " --> pdb=" O GLU f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 33 Processing helix chain 'g' and resid 81 through 104 Processing helix chain 'g' and resid 108 through 126 removed outlier: 3.731A pdb=" N LEU g 112 " --> pdb=" O ASN g 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR g 123 " --> pdb=" O GLN g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 180 Processing helix chain 'g' and resid 185 through 202 removed outlier: 3.537A pdb=" N SER g 200 " --> pdb=" O ALA g 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL g 229 " --> pdb=" O ASP g 225 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS g 230 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS g 231 " --> pdb=" O GLU g 227 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE g 232 " --> pdb=" O GLU g 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain '1' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain '2' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.616A pdb=" N ARG A 222 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.777A pdb=" N GLY A 80 " --> pdb=" O SER R 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.609A pdb=" N ARG B 222 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.936A pdb=" N GLY B 80 " --> pdb=" O SER S 231 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 231 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.709A pdb=" N GLY C 80 " --> pdb=" O SER T 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'D' and resid 67 through 71 removed outlier: 5.961A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 67 through 71 removed outlier: 5.961A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 80 " --> pdb=" O SER U 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.593A pdb=" N ARG E 222 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AC1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.528A pdb=" N GLY E 80 " --> pdb=" O SER O 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AC3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AC4, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.749A pdb=" N GLY F 80 " --> pdb=" O SER P 231 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AC6, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AC7, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.875A pdb=" N GLY G 80 " --> pdb=" O SER Q 231 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER Q 231 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 124 through 125 Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AD2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 124 through 125 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AD6, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 124 through 125 Processing sheet with id=AD8, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 124 through 125 Processing sheet with id=AE1, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 124 through 125 Processing sheet with id=AE3, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 124 through 125 Processing sheet with id=AE5, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 124 through 125 Processing sheet with id=AE7, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 124 through 125 Processing sheet with id=AE9, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 124 through 125 Processing sheet with id=AF2, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 124 through 125 Processing sheet with id=AF4, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 162 through 165 removed outlier: 3.504A pdb=" N ARG a 222 " --> pdb=" O SER a 214 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 67 through 71 removed outlier: 6.119A pdb=" N VAL a 74 " --> pdb=" O ILE a 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN a 158 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 162 through 165 removed outlier: 3.513A pdb=" N ARG b 222 " --> pdb=" O SER b 214 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 67 through 71 removed outlier: 6.083A pdb=" N VAL b 74 " --> pdb=" O ILE b 70 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU b 148 " --> pdb=" O TYR b 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN b 158 " --> pdb=" O ASP b 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 162 through 165 removed outlier: 3.507A pdb=" N ARG c 222 " --> pdb=" O SER c 214 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 67 through 71 removed outlier: 6.140A pdb=" N VAL c 74 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU c 148 " --> pdb=" O TYR c 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN c 158 " --> pdb=" O ASP c 150 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 162 through 165 removed outlier: 3.508A pdb=" N ARG d 222 " --> pdb=" O SER d 214 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 67 through 71 removed outlier: 6.128A pdb=" N VAL d 74 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN d 158 " --> pdb=" O ASP d 150 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 162 through 165 removed outlier: 3.511A pdb=" N ARG e 222 " --> pdb=" O SER e 214 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 67 through 71 removed outlier: 6.134A pdb=" N VAL e 74 " --> pdb=" O ILE e 70 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU e 148 " --> pdb=" O TYR e 160 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN e 158 " --> pdb=" O ASP e 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 162 through 165 removed outlier: 3.511A pdb=" N ARG f 222 " --> pdb=" O SER f 214 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 67 through 71 removed outlier: 6.144A pdb=" N VAL f 74 " --> pdb=" O ILE f 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN f 158 " --> pdb=" O ASP f 150 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 162 through 165 removed outlier: 3.506A pdb=" N ARG g 222 " --> pdb=" O SER g 214 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 67 through 71 removed outlier: 6.116A pdb=" N VAL g 74 " --> pdb=" O ILE g 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN g 158 " --> pdb=" O ASP g 150 " (cutoff:3.500A) 3550 hydrogen bonds defined for protein. 10290 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: 21.09 Time building geometry restraints manager: 18.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9999 1.31 - 1.43: 14050 1.43 - 1.56: 34397 1.56 - 1.69: 18 1.69 - 1.81: 448 Bond restraints: 58912 Sorted by residual: bond pdb=" CA LEU B 21 " pdb=" CB LEU B 21 " ideal model delta sigma weight residual 1.526 1.415 0.111 1.53e-02 4.27e+03 5.29e+01 bond pdb=" C VAL C 129 " pdb=" N ARG C 130 " ideal model delta sigma weight residual 1.327 1.244 0.083 1.71e-02 3.42e+03 2.33e+01 bond pdb=" CA LYS f 53 " pdb=" CB LYS f 53 " ideal model delta sigma weight residual 1.525 1.583 -0.058 1.47e-02 4.63e+03 1.58e+01 bond pdb=" CA LYS c 53 " pdb=" CB LYS c 53 " ideal model delta sigma weight residual 1.525 1.583 -0.058 1.47e-02 4.63e+03 1.56e+01 bond pdb=" CA LYS a 53 " pdb=" CB LYS a 53 " ideal model delta sigma weight residual 1.525 1.582 -0.058 1.47e-02 4.63e+03 1.54e+01 ... (remaining 58907 not shown) Histogram of bond angle deviations from ideal: 97.88 - 106.35: 1186 106.35 - 114.81: 35589 114.81 - 123.28: 40146 123.28 - 131.74: 2578 131.74 - 140.21: 42 Bond angle restraints: 79541 Sorted by residual: angle pdb=" C THR 2 21 " pdb=" N MET 2 22 " pdb=" CA MET 2 22 " ideal model delta sigma weight residual 121.70 140.21 -18.51 1.80e+00 3.09e-01 1.06e+02 angle pdb=" C THR K 21 " pdb=" N MET K 22 " pdb=" CA MET K 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR N 21 " pdb=" N MET N 22 " pdb=" CA MET N 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR 1 21 " pdb=" N MET 1 22 " pdb=" CA MET 1 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR Y 21 " pdb=" N MET Y 22 " pdb=" CA MET Y 22 " ideal model delta sigma weight residual 121.70 140.16 -18.46 1.80e+00 3.09e-01 1.05e+02 ... (remaining 79536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 34270 15.43 - 30.86: 1295 30.86 - 46.30: 382 46.30 - 61.73: 47 61.73 - 77.16: 35 Dihedral angle restraints: 36029 sinusoidal: 14350 harmonic: 21679 Sorted by residual: dihedral pdb=" CA ASN J 24 " pdb=" C ASN J 24 " pdb=" N PHE J 25 " pdb=" CA PHE J 25 " ideal model delta harmonic sigma weight residual 180.00 120.02 59.98 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " pdb=" CA PHE W 25 " ideal model delta harmonic sigma weight residual 180.00 120.03 59.97 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ASN 1 24 " pdb=" C ASN 1 24 " pdb=" N PHE 1 25 " pdb=" CA PHE 1 25 " ideal model delta harmonic sigma weight residual 180.00 120.04 59.96 0 5.00e+00 4.00e-02 1.44e+02 ... (remaining 36026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 8206 0.095 - 0.190: 987 0.190 - 0.285: 88 0.285 - 0.380: 15 0.380 - 0.475: 14 Chirality restraints: 9310 Sorted by residual: chirality pdb=" CB ILE W 178 " pdb=" CA ILE W 178 " pdb=" CG1 ILE W 178 " pdb=" CG2 ILE W 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE L 178 " pdb=" CA ILE L 178 " pdb=" CG1 ILE L 178 " pdb=" CG2 ILE L 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE M 178 " pdb=" CA ILE M 178 " pdb=" CG1 ILE M 178 " pdb=" CG2 ILE M 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 9307 not shown) Planarity restraints: 10206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 63 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C SER D 63 " 0.062 2.00e-02 2.50e+03 pdb=" O SER D 63 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 64 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 63 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C SER B 63 " -0.062 2.00e-02 2.50e+03 pdb=" O SER B 63 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 64 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 63 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER E 63 " 0.062 2.00e-02 2.50e+03 pdb=" O SER E 63 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE E 64 " -0.021 2.00e-02 2.50e+03 ... (remaining 10203 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 14073 2.79 - 3.32: 53747 3.32 - 3.84: 97557 3.84 - 4.37: 114962 4.37 - 4.90: 199233 Nonbonded interactions: 479572 Sorted by model distance: nonbonded pdb=" NH2 ARG H 70 " pdb=" OD1 ASN a 111 " model vdw 2.260 2.520 nonbonded pdb=" OG SER T 63 " pdb=" OG SER U 178 " model vdw 2.262 2.440 nonbonded pdb=" O GLY C 155 " pdb=" NH2 ARG D 86 " model vdw 2.272 2.520 nonbonded pdb=" NH2 ARG N 70 " pdb=" OD1 ASN g 111 " model vdw 2.273 2.520 nonbonded pdb=" NH2 ARG M 70 " pdb=" OD1 ASN f 111 " model vdw 2.273 2.520 ... (remaining 479567 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 '1' selection = chain '2' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'B' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'C' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'D' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'E' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'F' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'G' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'a' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'b' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'c' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'd' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'e' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'f' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'g' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.040 Extract box with map and model: 11.230 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 111.130 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 0.111 58912 Z= 0.608 Angle : 1.217 18.506 79541 Z= 0.698 Chirality : 0.066 0.475 9310 Planarity : 0.007 0.061 10206 Dihedral : 10.038 77.161 22155 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.05 % Favored : 94.57 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.08), residues: 7441 helix: -1.56 (0.07), residues: 3346 sheet: -1.17 (0.12), residues: 1379 loop : -2.71 (0.10), residues: 2716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2521 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 2472 time to evaluate : 4.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 2500 average time/residue: 0.5876 time to fit residues: 2383.1105 Evaluate side-chains 1383 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1351 time to evaluate : 5.117 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4033 time to fit residues: 31.6949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 8.9990 chunk 557 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 375 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 576 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 350 optimal weight: 8.9990 chunk 428 optimal weight: 0.8980 chunk 667 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 36 GLN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 ASN ** 2 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 186 GLN D 219 ASN H 88 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN J 98 GLN K 30 ASN K 88 ASN L 88 ASN M 30 ASN M 88 ASN N 88 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 GLN O 75 GLN O 111 HIS ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 HIS Q 111 HIS R 11 ASN R 72 GLN R 75 GLN R 111 HIS ** S 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 HIS U 111 HIS V 36 GLN V 85 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 GLN ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 GLN b 23 GLN c 23 GLN c 44 ASN c 108 ASN c 122 GLN d 23 GLN d 122 GLN e 23 GLN e 44 ASN f 23 GLN f 44 ASN f 122 GLN g 23 GLN g 44 ASN g 108 ASN g 122 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 58912 Z= 0.223 Angle : 0.709 12.758 79541 Z= 0.385 Chirality : 0.046 0.413 9310 Planarity : 0.005 0.060 10206 Dihedral : 6.322 53.490 8232 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.14 (0.09), residues: 7441 helix: 0.48 (0.08), residues: 3416 sheet: -0.76 (0.12), residues: 1358 loop : -2.36 (0.10), residues: 2667 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1612 time to evaluate : 4.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 287 outliers final: 158 residues processed: 1790 average time/residue: 0.5965 time to fit residues: 1797.8008 Evaluate side-chains 1435 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1277 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 158 outliers final: 0 residues processed: 158 average time/residue: 0.4306 time to fit residues: 136.7846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 555 optimal weight: 0.8980 chunk 454 optimal weight: 8.9990 chunk 184 optimal weight: 0.4980 chunk 668 optimal weight: 9.9990 chunk 722 optimal weight: 4.9990 chunk 595 optimal weight: 0.8980 chunk 663 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 536 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 141 GLN A 23 GLN A 61 GLN A 143 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN G 23 GLN H 88 ASN H 89 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN K 88 ASN L 88 ASN M 88 ASN N 98 GLN N 141 GLN O 47 HIS O 79 HIS P 11 ASN P 47 HIS P 72 GLN P 75 GLN P 79 HIS Q 79 HIS ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 HIS S 79 HIS T 11 ASN T 47 HIS T 79 HIS U 47 HIS V 141 GLN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN a 68 GLN ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN c 68 GLN d 68 GLN d 122 GLN e 122 GLN g 68 GLN g 219 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 58912 Z= 0.210 Angle : 0.683 13.887 79541 Z= 0.368 Chirality : 0.045 0.370 9310 Planarity : 0.004 0.055 10206 Dihedral : 5.863 53.615 8232 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.41 (0.09), residues: 7441 helix: 1.23 (0.08), residues: 3416 sheet: -0.61 (0.12), residues: 1358 loop : -2.11 (0.11), residues: 2667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1666 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1439 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 121 residues processed: 1573 average time/residue: 0.5332 time to fit residues: 1424.0599 Evaluate side-chains 1347 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1226 time to evaluate : 4.889 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 0 residues processed: 121 average time/residue: 0.4169 time to fit residues: 101.1582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 10.0000 chunk 502 optimal weight: 6.9990 chunk 347 optimal weight: 0.9980 chunk 74 optimal weight: 0.0050 chunk 319 optimal weight: 2.9990 chunk 449 optimal weight: 4.9990 chunk 671 optimal weight: 10.0000 chunk 710 optimal weight: 30.0000 chunk 350 optimal weight: 6.9990 chunk 636 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 61 GLN C 226 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN F 61 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN J 98 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN K 98 GLN L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN O 11 ASN P 11 ASN ** Q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 ASN R 79 HIS T 11 ASN U 79 HIS V 73 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN a 122 GLN b 44 ASN b 68 GLN b 219 ASN c 44 ASN c 68 GLN d 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 219 ASN e 44 ASN e 122 GLN e 219 ASN f 68 GLN ** f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 58912 Z= 0.431 Angle : 0.774 14.711 79541 Z= 0.413 Chirality : 0.049 0.435 9310 Planarity : 0.005 0.050 10206 Dihedral : 5.909 53.874 8232 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.16 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.26 (0.09), residues: 7441 helix: 1.37 (0.09), residues: 3416 sheet: -0.72 (0.12), residues: 1372 loop : -1.93 (0.11), residues: 2653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1301 time to evaluate : 4.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 284 outliers final: 187 residues processed: 1466 average time/residue: 0.5298 time to fit residues: 1317.6020 Evaluate side-chains 1319 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1132 time to evaluate : 4.935 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 0 residues processed: 187 average time/residue: 0.4042 time to fit residues: 150.7255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 2.9990 chunk 403 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 528 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 606 optimal weight: 2.9990 chunk 491 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 637 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN B 44 ASN D 226 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN H 88 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN J 98 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 88 ASN M 88 ASN N 88 ASN O 11 ASN P 11 ASN Q 47 HIS ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN b 219 ASN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 58912 Z= 0.197 Angle : 0.672 13.517 79541 Z= 0.362 Chirality : 0.045 0.395 9310 Planarity : 0.004 0.052 10206 Dihedral : 5.661 53.790 8232 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.19 (0.09), residues: 7441 helix: 1.80 (0.09), residues: 3416 sheet: -0.40 (0.12), residues: 1344 loop : -1.85 (0.11), residues: 2681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1360 time to evaluate : 5.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 59 residues processed: 1432 average time/residue: 0.5444 time to fit residues: 1314.2950 Evaluate side-chains 1286 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1227 time to evaluate : 5.049 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.4227 time to fit residues: 53.5381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 3.9990 chunk 639 optimal weight: 0.4980 chunk 140 optimal weight: 0.8980 chunk 417 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 711 optimal weight: 7.9990 chunk 590 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN E 143 GLN E 226 GLN F 97 GLN H 88 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 88 ASN M 88 ASN O 11 ASN P 11 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 58912 Z= 0.255 Angle : 0.673 13.418 79541 Z= 0.363 Chirality : 0.045 0.395 9310 Planarity : 0.004 0.060 10206 Dihedral : 5.564 53.407 8232 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.47 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.32 (0.10), residues: 7441 helix: 1.92 (0.09), residues: 3416 sheet: -0.47 (0.12), residues: 1372 loop : -1.74 (0.11), residues: 2653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1269 time to evaluate : 5.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 82 residues processed: 1339 average time/residue: 0.5751 time to fit residues: 1317.8516 Evaluate side-chains 1229 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1147 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.4355 time to fit residues: 74.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 405 optimal weight: 6.9990 chunk 519 optimal weight: 1.9990 chunk 402 optimal weight: 2.9990 chunk 598 optimal weight: 9.9990 chunk 397 optimal weight: 0.7980 chunk 708 optimal weight: 7.9990 chunk 443 optimal weight: 8.9990 chunk 431 optimal weight: 0.9980 chunk 327 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN K 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 GLN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 ASN f 68 GLN g 122 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 58912 Z= 0.224 Angle : 0.667 13.280 79541 Z= 0.359 Chirality : 0.045 0.376 9310 Planarity : 0.004 0.051 10206 Dihedral : 5.484 52.744 8232 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.51 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 7441 helix: 2.03 (0.09), residues: 3416 sheet: -0.35 (0.13), residues: 1358 loop : -1.73 (0.11), residues: 2667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1269 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 48 residues processed: 1328 average time/residue: 0.5445 time to fit residues: 1221.7086 Evaluate side-chains 1209 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1161 time to evaluate : 4.930 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4074 time to fit residues: 43.7714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 chunk 423 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 450 optimal weight: 0.7980 chunk 482 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 556 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN D 97 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN K 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 ASN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 ASN b 125 GLN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 122 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 58912 Z= 0.243 Angle : 0.682 13.415 79541 Z= 0.365 Chirality : 0.045 0.343 9310 Planarity : 0.004 0.106 10206 Dihedral : 5.488 53.109 8232 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.47 (0.10), residues: 7441 helix: 2.03 (0.09), residues: 3423 sheet: -0.38 (0.13), residues: 1323 loop : -1.63 (0.11), residues: 2695 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1234 time to evaluate : 5.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 56 residues processed: 1282 average time/residue: 0.5410 time to fit residues: 1173.6595 Evaluate side-chains 1210 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1154 time to evaluate : 4.909 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4011 time to fit residues: 50.3600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 20.0000 chunk 678 optimal weight: 4.9990 chunk 619 optimal weight: 2.9990 chunk 660 optimal weight: 7.9990 chunk 397 optimal weight: 0.8980 chunk 287 optimal weight: 2.9990 chunk 518 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 596 optimal weight: 10.0000 chunk 624 optimal weight: 10.0000 chunk 657 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 ASN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN f 68 GLN g 122 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 58912 Z= 0.251 Angle : 0.694 13.499 79541 Z= 0.370 Chirality : 0.046 0.369 9310 Planarity : 0.004 0.055 10206 Dihedral : 5.483 53.080 8232 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.52 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 (0.10), residues: 7441 helix: 2.00 (0.09), residues: 3430 sheet: -0.47 (0.13), residues: 1365 loop : -1.60 (0.12), residues: 2646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1225 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 36 residues processed: 1262 average time/residue: 0.5460 time to fit residues: 1167.9691 Evaluate side-chains 1180 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1144 time to evaluate : 5.103 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4182 time to fit residues: 35.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 8.9990 chunk 698 optimal weight: 3.9990 chunk 426 optimal weight: 0.9990 chunk 331 optimal weight: 0.7980 chunk 485 optimal weight: 3.9990 chunk 732 optimal weight: 20.0000 chunk 673 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 450 optimal weight: 0.7980 chunk 357 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN W 36 GLN W 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 ASN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 ASN f 68 GLN f 125 GLN f 183 ASN f 219 ASN g 122 GLN g 183 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 58912 Z= 0.256 Angle : 0.712 13.620 79541 Z= 0.378 Chirality : 0.046 0.382 9310 Planarity : 0.004 0.089 10206 Dihedral : 5.504 53.202 8232 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.47 (0.10), residues: 7441 helix: 2.00 (0.09), residues: 3423 sheet: -0.49 (0.13), residues: 1365 loop : -1.55 (0.12), residues: 2653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1205 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 31 residues processed: 1228 average time/residue: 0.5543 time to fit residues: 1148.4606 Evaluate side-chains 1146 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1115 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4049 time to fit residues: 30.8621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 2.9990 chunk 621 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 537 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 584 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 599 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN a 183 ASN b 44 ASN c 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 122 GLN ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099229 restraints weight = 89661.265| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.20 r_work: 0.3108 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 58912 Z= 0.258 Angle : 0.724 13.660 79541 Z= 0.385 Chirality : 0.046 0.382 9310 Planarity : 0.004 0.082 10206 Dihedral : 5.511 53.243 8232 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.36 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.47 (0.10), residues: 7441 helix: 1.99 (0.09), residues: 3416 sheet: -0.49 (0.13), residues: 1365 loop : -1.51 (0.12), residues: 2660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19486.87 seconds wall clock time: 339 minutes 33.38 seconds (20373.38 seconds total)