Starting phenix.real_space_refine (version: dev) on Fri May 13 09:50:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/05_2022/6r6b_4734.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 11416 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 180, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1340 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 2 Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1332 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 Chain: "E" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1348 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain breaks: 2 Chain: "F" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1923 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "I" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "H" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "J" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Time building chain proxies: 6.37, per 1000 atoms: 0.56 Number of scatterers: 11416 At special positions: 0 Unit cell: (92.886, 92.886, 124.944, 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 74 16.00 O 1939 8.00 N 1700 7.00 C 7703 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: 4.85 Conformation dependent library (CDL) restraints added in 1.7 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.610A pdb=" N PHE A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 78 removed outlier: 3.917A pdb=" N GLY A 54 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.812A pdb=" N ALA A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.761A pdb=" N ILE A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.561A pdb=" N HIS A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.285A pdb=" N ILE A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.909A pdb=" N PHE A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.930A pdb=" N LEU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.740A pdb=" N PHE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.722A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Proline residue: B 66 - end of helix removed outlier: 3.883A pdb=" N ALA B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.163A pdb=" N LYS B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.533A pdb=" N ARG B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 174 removed outlier: 3.620A pdb=" N LEU B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix removed outlier: 3.565A pdb=" N VAL B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 4.497A pdb=" N ILE B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.769A pdb=" N PHE B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.747A pdb=" N PHE C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 Proline residue: C 66 - end of helix Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.717A pdb=" N LYS C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 removed outlier: 3.712A pdb=" N ARG C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 175 Proline residue: C 160 - end of helix removed outlier: 3.638A pdb=" N VAL C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.653A pdb=" N VAL C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 188 - end of helix removed outlier: 3.716A pdb=" N PHE C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.530A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 25 removed outlier: 3.513A pdb=" N THR D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.642A pdb=" N PHE D 30 " --> pdb=" O CYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 49 through 64 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.631A pdb=" N ALA D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.538A pdb=" N HIS D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.795A pdb=" N ARG D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 175 Proline residue: D 160 - end of helix removed outlier: 3.612A pdb=" N VAL D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 removed outlier: 4.592A pdb=" N ILE D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.973A pdb=" N PHE D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 209 Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.522A pdb=" N PHE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 25 removed outlier: 4.509A pdb=" N ALA E 23 " --> pdb=" O PHE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 41 removed outlier: 3.617A pdb=" N PHE E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 72 removed outlier: 4.173A pdb=" N LEU E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 97 through 107 removed outlier: 3.723A pdb=" N HIS E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.518A pdb=" N ARG E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 175 removed outlier: 3.537A pdb=" N LEU E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 159 " --> pdb=" O PHE E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix removed outlier: 3.500A pdb=" N VAL E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 Proline residue: E 188 - end of helix removed outlier: 3.995A pdb=" N PHE E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 209 removed outlier: 4.141A pdb=" N ALA E 206 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 removed outlier: 3.875A pdb=" N ILE F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 17 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 56 removed outlier: 4.445A pdb=" N ILE F 45 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.750A pdb=" N SER F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 90 removed outlier: 3.954A pdb=" N PHE F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.748A pdb=" N SER F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 141 removed outlier: 3.519A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.531A pdb=" N PHE F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 206 removed outlier: 3.631A pdb=" N ALA F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Proline residue: F 188 - end of helix removed outlier: 3.711A pdb=" N ILE F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL F 192 " --> pdb=" O PRO F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.554A pdb=" N ILE F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 222 " --> pdb=" O THR F 218 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 removed outlier: 4.365A pdb=" N GLN F 241 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 35 removed outlier: 3.793A pdb=" N TRP I 21 " --> pdb=" O ILE I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 48 through 62 removed outlier: 5.383A pdb=" N ILE I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 84 removed outlier: 4.268A pdb=" N LEU I 71 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET I 79 " --> pdb=" O CYS I 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 20 removed outlier: 3.636A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 36 Processing helix chain 'G' and resid 48 through 62 removed outlier: 4.512A pdb=" N ILE G 54 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 4.127A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 20 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 46 through 62 removed outlier: 4.548A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 82 removed outlier: 4.094A pdb=" N LEU H 71 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 18 Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.568A pdb=" N VAL J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 62 removed outlier: 3.881A pdb=" N GLY J 50 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 54 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 70 through 82 675 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3237 1.34 - 1.46: 2874 1.46 - 1.58: 5421 1.58 - 1.70: 1 1.70 - 1.82: 135 Bond restraints: 11668 Sorted by residual: bond pdb=" C LEU A 109 " pdb=" N GLU A 110 " ideal model delta sigma weight residual 1.334 1.467 -0.133 1.61e-02 3.86e+03 6.86e+01 bond pdb=" CA VAL F 67 " pdb=" C VAL F 67 " ideal model delta sigma weight residual 1.523 1.590 -0.067 1.27e-02 6.20e+03 2.78e+01 bond pdb=" C LEU C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.73e+01 bond pdb=" N VAL F 67 " pdb=" CA VAL F 67 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.48e+01 bond pdb=" C LEU J 47 " pdb=" N PRO J 48 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 ... (remaining 11663 not shown) Histogram of bond angle deviations from ideal: 93.14 - 105.35: 247 105.35 - 117.55: 8081 117.55 - 129.76: 7402 129.76 - 141.97: 83 141.97 - 154.18: 1 Bond angle restraints: 15814 Sorted by residual: angle pdb=" C VAL F 67 " pdb=" N PHE F 68 " pdb=" CA PHE F 68 " ideal model delta sigma weight residual 126.86 154.18 -27.32 1.57e+00 4.06e-01 3.03e+02 angle pdb=" C SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta sigma weight residual 110.67 127.27 -16.60 1.92e+00 2.71e-01 7.47e+01 angle pdb=" N LYS H 83 " pdb=" CA LYS H 83 " pdb=" C LYS H 83 " ideal model delta sigma weight residual 113.38 103.69 9.69 1.23e+00 6.61e-01 6.21e+01 angle pdb=" N SER F 66 " pdb=" CA SER F 66 " pdb=" C SER F 66 " ideal model delta sigma weight residual 108.76 121.99 -13.23 1.69e+00 3.50e-01 6.12e+01 angle pdb=" N ILE C 67 " pdb=" CA ILE C 67 " pdb=" C ILE C 67 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 6090 13.92 - 27.85: 538 27.85 - 41.77: 188 41.77 - 55.70: 36 55.70 - 69.62: 3 Dihedral angle restraints: 6855 sinusoidal: 2640 harmonic: 4215 Sorted by residual: dihedral pdb=" C SER F 86 " pdb=" N SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta harmonic sigma weight residual -122.60 -146.11 23.51 0 2.50e+00 1.60e-01 8.84e+01 dihedral pdb=" CA THR G 38 " pdb=" C THR G 38 " pdb=" N VAL G 39 " pdb=" CA VAL G 39 " ideal model delta harmonic sigma weight residual -180.00 -139.00 -41.00 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA GLY I 68 " pdb=" C GLY I 68 " pdb=" N GLU I 69 " pdb=" CA GLU I 69 " ideal model delta harmonic sigma weight residual -180.00 -146.02 -33.98 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1890 0.166 - 0.332: 36 0.332 - 0.498: 0 0.498 - 0.664: 0 0.664 - 0.830: 1 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CA SER F 86 " pdb=" N SER F 86 " pdb=" C SER F 86 " pdb=" CB SER F 86 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA VAL C 46 " pdb=" N VAL C 46 " pdb=" C VAL C 46 " pdb=" CB VAL C 46 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 51 " pdb=" CA ILE G 51 " pdb=" CG1 ILE G 51 " pdb=" CG2 ILE G 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1924 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.033 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C LEU A 109 " 0.106 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.039 2.00e-02 2.50e+03 pdb=" N GLU A 110 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 62 " -0.028 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C ASP F 62 " 0.102 2.00e-02 2.50e+03 pdb=" O ASP F 62 " -0.041 2.00e-02 2.50e+03 pdb=" N ILE F 63 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 67 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C VAL F 67 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL F 67 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE F 68 " 0.024 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 30 2.40 - 3.02: 5866 3.02 - 3.65: 17695 3.65 - 4.27: 25556 4.27 - 4.90: 42126 Nonbonded interactions: 91273 Sorted by model distance: nonbonded pdb=" O PHE A 115 " pdb=" OG SER A 137 " model vdw 1.771 2.440 nonbonded pdb=" OE1 GLU B 209 " pdb=" CE LYS H 83 " model vdw 1.812 3.440 nonbonded pdb=" OE1 GLU B 209 " pdb=" CD LYS H 83 " model vdw 1.926 3.440 nonbonded pdb=" OG SER A 134 " pdb=" N LEU A 135 " model vdw 2.120 2.520 nonbonded pdb=" O GLY A 24 " pdb=" OH TYR A 99 " model vdw 2.260 2.440 ... (remaining 91268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'B' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'C' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'D' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'E' and (resid 11 through 116 or resid 133 through 213)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7703 2.51 5 N 1700 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.950 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 32.100 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.010 0.133 11668 Z= 0.644 Angle : 1.362 27.323 15814 Z= 0.693 Chirality : 0.067 0.830 1927 Planarity : 0.009 0.071 1877 Dihedral : 12.493 69.623 4135 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.56 % Favored : 91.09 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -5.15 (0.17), residues: 1414 helix: -3.10 (0.11), residues: 1064 sheet: None (None), residues: 0 loop : -3.66 (0.30), residues: 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 531 time to evaluate : 1.354 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 outliers start: 25 outliers final: 2 residues processed: 546 average time/residue: 0.2247 time to fit residues: 172.5099 Evaluate side-chains 301 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1262 time to fit residues: 2.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0970 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 101 GLN F 106 GLN F 247 HIS ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 11668 Z= 0.244 Angle : 0.915 13.150 15814 Z= 0.443 Chirality : 0.046 0.183 1927 Planarity : 0.006 0.060 1877 Dihedral : 6.140 32.352 1515 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.07 % Favored : 92.72 % Rotamer Outliers : 5.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.20), residues: 1414 helix: -1.56 (0.14), residues: 1101 sheet: None (None), residues: 0 loop : -3.51 (0.33), residues: 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 358 time to evaluate : 1.405 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 outliers start: 72 outliers final: 28 residues processed: 412 average time/residue: 0.2066 time to fit residues: 123.2950 Evaluate side-chains 327 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 299 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1221 time to fit residues: 8.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.0010 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS E 101 GLN I 9 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11668 Z= 0.258 Angle : 0.864 12.185 15814 Z= 0.421 Chirality : 0.045 0.181 1927 Planarity : 0.005 0.062 1877 Dihedral : 5.690 27.604 1515 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.21 % Favored : 92.57 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.22), residues: 1414 helix: -0.83 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -3.11 (0.37), residues: 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 331 time to evaluate : 1.486 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 outliers start: 45 outliers final: 16 residues processed: 359 average time/residue: 0.1951 time to fit residues: 102.8204 Evaluate side-chains 310 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 294 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1005 time to fit residues: 4.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 40.0000 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 112 optimal weight: 0.0980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 53 ASN ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11668 Z= 0.221 Angle : 0.826 11.113 15814 Z= 0.398 Chirality : 0.043 0.195 1927 Planarity : 0.005 0.064 1877 Dihedral : 5.466 32.476 1515 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.00 % Favored : 92.86 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.53 (0.23), residues: 1414 helix: -0.42 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 333 time to evaluate : 1.456 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 outliers start: 38 outliers final: 15 residues processed: 357 average time/residue: 0.2006 time to fit residues: 105.1306 Evaluate side-chains 309 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 294 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1081 time to fit residues: 4.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 11668 Z= 0.236 Angle : 0.830 9.645 15814 Z= 0.402 Chirality : 0.044 0.207 1927 Planarity : 0.005 0.065 1877 Dihedral : 5.288 27.780 1515 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.14 % Favored : 92.72 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1414 helix: -0.20 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -2.70 (0.38), residues: 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 1.327 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 outliers start: 16 outliers final: 5 residues processed: 335 average time/residue: 0.1953 time to fit residues: 98.0101 Evaluate side-chains 306 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 301 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1027 time to fit residues: 2.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 0.0470 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN I 9 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 11668 Z= 0.218 Angle : 0.848 14.531 15814 Z= 0.404 Chirality : 0.043 0.213 1927 Planarity : 0.005 0.067 1877 Dihedral : 5.204 25.336 1515 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.79 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1414 helix: -0.09 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 329 time to evaluate : 1.363 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 outliers start: 31 outliers final: 14 residues processed: 348 average time/residue: 0.1932 time to fit residues: 100.0484 Evaluate side-chains 317 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 303 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1157 time to fit residues: 4.6766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 134 optimal weight: 0.0010 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 11668 Z= 0.260 Angle : 0.895 15.309 15814 Z= 0.424 Chirality : 0.044 0.214 1927 Planarity : 0.006 0.111 1877 Dihedral : 5.165 24.545 1515 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.14 % Favored : 92.79 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1414 helix: 0.05 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 331 average time/residue: 0.1944 time to fit residues: 96.4819 Evaluate side-chains 293 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 287 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1299 time to fit residues: 3.1901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 11668 Z= 0.230 Angle : 0.923 16.391 15814 Z= 0.432 Chirality : 0.046 0.381 1927 Planarity : 0.006 0.107 1877 Dihedral : 5.151 22.039 1515 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1414 helix: 0.10 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.63 (0.39), residues: 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 305 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 311 average time/residue: 0.1953 time to fit residues: 90.5823 Evaluate side-chains 294 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 287 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1023 time to fit residues: 2.9145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.140 11668 Z= 0.363 Angle : 0.975 15.453 15814 Z= 0.465 Chirality : 0.047 0.252 1927 Planarity : 0.006 0.107 1877 Dihedral : 5.157 25.391 1515 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1414 helix: 0.18 (0.16), residues: 1126 sheet: None (None), residues: 0 loop : -2.83 (0.41), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 299 average time/residue: 0.1902 time to fit residues: 85.5560 Evaluate side-chains 288 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 281 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1048 time to fit residues: 3.1471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.140 11668 Z= 0.262 Angle : 0.990 15.436 15814 Z= 0.466 Chirality : 0.046 0.236 1927 Planarity : 0.006 0.122 1877 Dihedral : 5.199 24.469 1515 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1414 helix: 0.22 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -2.81 (0.40), residues: 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 299 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 299 average time/residue: 0.1914 time to fit residues: 85.5025 Evaluate side-chains 286 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1325 time to fit residues: 2.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.0060 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050669 restraints weight = 48930.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052276 restraints weight = 27374.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053448 restraints weight = 18991.841| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 11668 Z= 0.263 Angle : 1.011 16.723 15814 Z= 0.470 Chirality : 0.046 0.233 1927 Planarity : 0.006 0.099 1877 Dihedral : 5.120 23.402 1515 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1414 helix: 0.25 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 305 =============================================================================== Job complete usr+sys time: 2495.40 seconds wall clock time: 46 minutes 10.07 seconds (2770.07 seconds total)