Starting phenix.real_space_refine on Tue Jul 29 08:58:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_4734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_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/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_4734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_4734.map" model { file = "/net/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_4734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r6b_4734/07_2025/6r6b_4734.cif" } resolution = 3.5 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= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180} 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: 7.47, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 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: 0.91 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: 2.86 Time building geometry restraints manager: 3.25 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: 0.00 - 5.46: 15638 5.46 - 10.93: 167 10.93 - 16.39: 7 16.39 - 21.86: 1 21.86 - 27.32: 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 3.040 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 3.120 nonbonded pdb=" O GLY A 24 " pdb=" OH TYR A 99 " model vdw 2.260 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.410 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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= 0.413 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 % Allowed : 6.54 % Favored : 91.50 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 200 HIS 0.007 0.002 HIS B 106 PHE 0.037 0.003 PHE F 133 TYR 0.024 0.003 TYR D 133 ARG 0.010 0.002 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.20668 ( 675) hydrogen bonds : angle 8.66439 ( 2019) covalent geometry : bond 0.01001 (11668) covalent geometry : angle 1.36174 (15814) *********************** 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 to be fit. rotamer outliers: 25 poor density : 531 time to evaluate : 1.433 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: A 190 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7752 (mtpt) REVERT: B 29 LYS cc_start: 0.7992 (tptt) cc_final: 0.7520 (tptm) REVERT: B 172 LEU cc_start: 0.7698 (tt) cc_final: 0.7131 (tt) REVERT: C 175 LEU cc_start: 0.8309 (tp) cc_final: 0.8045 (tt) REVERT: C 177 MET cc_start: 0.6125 (ptp) cc_final: 0.5719 (ptm) REVERT: D 197 LEU cc_start: 0.6869 (tp) cc_final: 0.6582 (tt) REVERT: I 59 SER cc_start: 0.8387 (p) cc_final: 0.8119 (t) REVERT: G 46 THR cc_start: 0.7333 (p) cc_final: 0.7042 (p) REVERT: G 59 SER cc_start: 0.7745 (p) cc_final: 0.7399 (t) outliers start: 25 outliers final: 2 residues processed: 546 average time/residue: 0.2543 time to fit residues: 195.8437 Evaluate side-chains 304 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 302 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 21 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 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: 0.9980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** D 44 GLN D 101 GLN F 106 GLN F 156 ASN F 247 HIS ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051416 restraints weight = 47059.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053041 restraints weight = 26588.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054055 restraints weight = 18495.878| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11668 Z= 0.174 Angle : 0.907 12.932 15814 Z= 0.444 Chirality : 0.046 0.175 1927 Planarity : 0.006 0.059 1877 Dihedral : 6.283 45.503 1518 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 5.12 % Allowed : 19.76 % Favored : 75.12 % 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: -3.03 (0.20), residues: 1414 helix: -1.48 (0.14), residues: 1082 sheet: None (None), residues: 0 loop : -3.27 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 200 HIS 0.012 0.001 HIS F 247 PHE 0.024 0.002 PHE F 76 TYR 0.023 0.002 TYR C 27 ARG 0.008 0.001 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 675) hydrogen bonds : angle 5.24428 ( 2019) covalent geometry : bond 0.00390 (11668) covalent geometry : angle 0.90663 (15814) *********************** 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 to be fit. rotamer outliers: 65 poor density : 365 time to evaluate : 1.225 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: A 36 MET cc_start: 0.9158 (ttm) cc_final: 0.8899 (ttm) REVERT: A 49 ASN cc_start: 0.8806 (t0) cc_final: 0.8548 (t0) REVERT: A 178 MET cc_start: 0.8078 (ppp) cc_final: 0.7424 (ppp) REVERT: B 46 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 158 TYR cc_start: 0.8835 (t80) cc_final: 0.8399 (t80) REVERT: B 179 MET cc_start: 0.7987 (tpp) cc_final: 0.7784 (tpp) REVERT: C 178 MET cc_start: 0.8224 (ppp) cc_final: 0.7342 (ppp) REVERT: C 198 ASP cc_start: 0.8264 (t0) cc_final: 0.8007 (t70) REVERT: D 50 MET cc_start: 0.8746 (tmm) cc_final: 0.8458 (tmm) REVERT: D 64 MET cc_start: 0.9274 (mmp) cc_final: 0.9016 (mmp) REVERT: D 142 TYR cc_start: 0.8181 (t80) cc_final: 0.7783 (t80) REVERT: D 146 GLU cc_start: 0.9502 (OUTLIER) cc_final: 0.9275 (mt-10) REVERT: D 149 ASP cc_start: 0.9232 (t0) cc_final: 0.8990 (t0) REVERT: D 178 MET cc_start: 0.7889 (ppp) cc_final: 0.6603 (ppp) REVERT: D 179 MET cc_start: 0.8253 (mmm) cc_final: 0.7456 (mpp) REVERT: E 36 MET cc_start: 0.9164 (ttm) cc_final: 0.8946 (ttm) REVERT: E 64 MET cc_start: 0.9406 (mmp) cc_final: 0.9202 (mmp) REVERT: E 177 MET cc_start: 0.8962 (pmm) cc_final: 0.8510 (pmm) REVERT: E 180 MET cc_start: 0.7695 (ppp) cc_final: 0.7159 (ppp) REVERT: E 205 LYS cc_start: 0.8944 (tmmt) cc_final: 0.8561 (tptm) REVERT: F 83 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9389 (tt) REVERT: F 87 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: F 144 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: F 220 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8965 (tmmt) REVERT: I 72 LEU cc_start: 0.9533 (tt) cc_final: 0.9296 (mm) REVERT: H 59 SER cc_start: 0.9531 (t) cc_final: 0.9313 (p) REVERT: J 7 MET cc_start: 0.8730 (mmt) cc_final: 0.8427 (mmt) REVERT: J 79 MET cc_start: 0.8990 (ppp) cc_final: 0.8672 (ppp) outliers start: 65 outliers final: 21 residues processed: 414 average time/residue: 0.2057 time to fit residues: 123.8139 Evaluate side-chains 328 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 43 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 = 0.3404 r_free = 0.3404 target = 0.067746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052100 restraints weight = 48719.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053689 restraints weight = 26778.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054651 restraints weight = 18510.731| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11668 Z= 0.169 Angle : 0.855 11.523 15814 Z= 0.418 Chirality : 0.045 0.212 1927 Planarity : 0.005 0.069 1877 Dihedral : 5.649 43.903 1516 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 4.96 % Allowed : 23.07 % Favored : 71.97 % 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: -1.98 (0.22), residues: 1414 helix: -0.72 (0.15), residues: 1089 sheet: None (None), residues: 0 loop : -2.97 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 200 HIS 0.003 0.001 HIS E 106 PHE 0.025 0.002 PHE G 49 TYR 0.026 0.002 TYR E 27 ARG 0.009 0.001 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 675) hydrogen bonds : angle 4.92206 ( 2019) covalent geometry : bond 0.00394 (11668) covalent geometry : angle 0.85464 (15814) *********************** 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 396 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 333 time to evaluate : 1.377 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: A 171 ILE cc_start: 0.9546 (pt) cc_final: 0.9325 (pt) REVERT: A 175 LEU cc_start: 0.9333 (tp) cc_final: 0.9121 (tp) REVERT: A 179 MET cc_start: 0.7726 (tpp) cc_final: 0.7450 (tpp) REVERT: B 45 GLN cc_start: 0.8813 (tp40) cc_final: 0.8604 (tp-100) REVERT: B 46 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8061 (p) REVERT: B 108 ASP cc_start: 0.8723 (t0) cc_final: 0.8108 (t0) REVERT: B 149 ASP cc_start: 0.8967 (t0) cc_final: 0.8613 (t0) REVERT: C 27 TYR cc_start: 0.9454 (t80) cc_final: 0.9228 (t80) REVERT: C 50 MET cc_start: 0.8412 (tpt) cc_final: 0.8204 (tpt) REVERT: C 135 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7703 (pp) REVERT: C 175 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 177 MET cc_start: 0.8692 (ppp) cc_final: 0.8241 (pmm) REVERT: C 178 MET cc_start: 0.8262 (ppp) cc_final: 0.7937 (ppp) REVERT: C 198 ASP cc_start: 0.8219 (t0) cc_final: 0.7966 (t70) REVERT: D 50 MET cc_start: 0.8727 (tmm) cc_final: 0.8504 (tmm) REVERT: D 64 MET cc_start: 0.9348 (mmp) cc_final: 0.9046 (mmp) REVERT: D 142 TYR cc_start: 0.8235 (t80) cc_final: 0.7936 (t80) REVERT: D 146 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9218 (mt-10) REVERT: D 149 ASP cc_start: 0.9258 (t0) cc_final: 0.8909 (t0) REVERT: D 179 MET cc_start: 0.8402 (mmm) cc_final: 0.8119 (mmm) REVERT: D 190 LYS cc_start: 0.9372 (mtmt) cc_final: 0.8992 (mtmm) REVERT: D 197 LEU cc_start: 0.8779 (tt) cc_final: 0.8509 (mt) REVERT: E 64 MET cc_start: 0.9495 (mmp) cc_final: 0.9289 (mmp) REVERT: E 180 MET cc_start: 0.7741 (ppp) cc_final: 0.7375 (ppp) REVERT: E 205 LYS cc_start: 0.8968 (tmmt) cc_final: 0.8748 (tptm) REVERT: F 83 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9365 (tt) REVERT: F 87 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: F 220 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9074 (tmmt) REVERT: F 227 ILE cc_start: 0.9809 (mm) cc_final: 0.9608 (tt) REVERT: I 19 SER cc_start: 0.9567 (t) cc_final: 0.9195 (p) REVERT: I 72 LEU cc_start: 0.9591 (tt) cc_final: 0.9354 (mm) REVERT: H 3 ASP cc_start: 0.8943 (p0) cc_final: 0.8675 (p0) REVERT: H 4 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9221 (mp) REVERT: J 79 MET cc_start: 0.9188 (ppp) cc_final: 0.8835 (ppp) outliers start: 63 outliers final: 27 residues processed: 374 average time/residue: 0.2091 time to fit residues: 114.3571 Evaluate side-chains 326 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 106 HIS ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049728 restraints weight = 49085.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051275 restraints weight = 26971.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052391 restraints weight = 18411.148| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11668 Z= 0.173 Angle : 0.832 11.059 15814 Z= 0.406 Chirality : 0.044 0.185 1927 Planarity : 0.005 0.058 1877 Dihedral : 5.425 44.874 1516 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 4.25 % Allowed : 25.04 % Favored : 70.71 % 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: -1.43 (0.23), residues: 1414 helix: -0.33 (0.16), residues: 1089 sheet: None (None), residues: 0 loop : -2.75 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 200 HIS 0.003 0.001 HIS E 106 PHE 0.017 0.001 PHE H 49 TYR 0.020 0.002 TYR E 27 ARG 0.004 0.001 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 675) hydrogen bonds : angle 4.70117 ( 2019) covalent geometry : bond 0.00408 (11668) covalent geometry : angle 0.83203 (15814) *********************** 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 372 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 1.384 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: A 36 MET cc_start: 0.9153 (ttm) cc_final: 0.8884 (ttm) REVERT: A 175 LEU cc_start: 0.9469 (tp) cc_final: 0.9213 (tp) REVERT: B 45 GLN cc_start: 0.8963 (tp40) cc_final: 0.8649 (tp-100) REVERT: B 108 ASP cc_start: 0.8674 (t0) cc_final: 0.8430 (t0) REVERT: B 111 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9039 (tt) REVERT: B 149 ASP cc_start: 0.8973 (t0) cc_final: 0.8496 (t0) REVERT: B 179 MET cc_start: 0.8717 (mmm) cc_final: 0.7535 (mmm) REVERT: C 27 TYR cc_start: 0.9492 (t80) cc_final: 0.9280 (t80) REVERT: C 50 MET cc_start: 0.8393 (tpt) cc_final: 0.8071 (tpt) REVERT: C 135 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7733 (pp) REVERT: C 177 MET cc_start: 0.8672 (ppp) cc_final: 0.8440 (ppp) REVERT: C 179 MET cc_start: 0.8835 (mmm) cc_final: 0.8571 (mmm) REVERT: C 198 ASP cc_start: 0.8384 (t0) cc_final: 0.8132 (t70) REVERT: D 50 MET cc_start: 0.8810 (tmm) cc_final: 0.8548 (tmm) REVERT: D 142 TYR cc_start: 0.8388 (t80) cc_final: 0.8085 (t80) REVERT: D 149 ASP cc_start: 0.9324 (t0) cc_final: 0.8936 (t0) REVERT: D 190 LYS cc_start: 0.9378 (mtmt) cc_final: 0.9046 (mtmm) REVERT: E 39 ASN cc_start: 0.9074 (m-40) cc_final: 0.8677 (m110) REVERT: E 180 MET cc_start: 0.8019 (ppp) cc_final: 0.7406 (ppp) REVERT: E 205 LYS cc_start: 0.8982 (tmmt) cc_final: 0.8604 (tptm) REVERT: F 35 ASN cc_start: 0.7208 (t0) cc_final: 0.6284 (m110) REVERT: F 83 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9326 (tt) REVERT: F 87 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: F 220 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8957 (tmmt) REVERT: I 19 SER cc_start: 0.9615 (t) cc_final: 0.9333 (p) REVERT: I 72 LEU cc_start: 0.9592 (tt) cc_final: 0.9353 (mm) REVERT: G 37 GLN cc_start: 0.9324 (mm110) cc_final: 0.8999 (mp10) REVERT: G 52 LYS cc_start: 0.9525 (mtmt) cc_final: 0.9275 (ttpp) REVERT: H 3 ASP cc_start: 0.9058 (p0) cc_final: 0.8785 (p0) REVERT: H 4 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9180 (mp) REVERT: H 45 GLN cc_start: 0.8958 (pm20) cc_final: 0.8165 (mt0) REVERT: H 49 PHE cc_start: 0.8924 (t80) cc_final: 0.8719 (t80) REVERT: H 52 LYS cc_start: 0.9576 (ptmt) cc_final: 0.9256 (ptpp) REVERT: J 79 MET cc_start: 0.9196 (ppp) cc_final: 0.8950 (ppp) outliers start: 54 outliers final: 21 residues processed: 355 average time/residue: 0.2432 time to fit residues: 128.0172 Evaluate side-chains 320 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 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 = 0.3349 r_free = 0.3349 target = 0.066558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051173 restraints weight = 47539.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052855 restraints weight = 25921.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053996 restraints weight = 17628.204| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11668 Z= 0.146 Angle : 0.826 13.613 15814 Z= 0.399 Chirality : 0.044 0.194 1927 Planarity : 0.004 0.064 1877 Dihedral : 5.281 45.821 1516 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.08 % Favored : 93.78 % Rotamer: Outliers : 3.86 % Allowed : 26.77 % Favored : 69.37 % 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: -1.11 (0.23), residues: 1414 helix: -0.15 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : -2.48 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 200 HIS 0.001 0.000 HIS E 106 PHE 0.014 0.001 PHE F 33 TYR 0.034 0.002 TYR A 158 ARG 0.006 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 675) hydrogen bonds : angle 4.57763 ( 2019) covalent geometry : bond 0.00339 (11668) covalent geometry : angle 0.82644 (15814) *********************** 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 372 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 1.200 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: A 36 MET cc_start: 0.9097 (ttm) cc_final: 0.8872 (ttm) REVERT: A 50 MET cc_start: 0.9044 (tpp) cc_final: 0.8699 (tpt) REVERT: A 93 ASP cc_start: 0.8886 (m-30) cc_final: 0.8493 (p0) REVERT: A 98 GLU cc_start: 0.8422 (pp20) cc_final: 0.8078 (pp20) REVERT: A 171 ILE cc_start: 0.9564 (pt) cc_final: 0.9235 (pt) REVERT: A 175 LEU cc_start: 0.9528 (tp) cc_final: 0.9163 (pp) REVERT: B 45 GLN cc_start: 0.8887 (tp40) cc_final: 0.8557 (tp-100) REVERT: B 108 ASP cc_start: 0.8734 (t0) cc_final: 0.8409 (t0) REVERT: B 111 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 149 ASP cc_start: 0.8952 (t0) cc_final: 0.8415 (t0) REVERT: B 179 MET cc_start: 0.8838 (mmm) cc_final: 0.8377 (mmm) REVERT: C 50 MET cc_start: 0.8469 (tpt) cc_final: 0.8262 (tpt) REVERT: C 135 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7642 (pp) REVERT: C 179 MET cc_start: 0.8941 (mmm) cc_final: 0.8523 (mmm) REVERT: C 198 ASP cc_start: 0.8350 (t0) cc_final: 0.8103 (t70) REVERT: D 50 MET cc_start: 0.8828 (tmm) cc_final: 0.8611 (tmm) REVERT: D 64 MET cc_start: 0.9302 (mmp) cc_final: 0.8981 (mmm) REVERT: D 142 TYR cc_start: 0.8204 (t80) cc_final: 0.7897 (t80) REVERT: D 146 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9154 (mt-10) REVERT: D 149 ASP cc_start: 0.9261 (t0) cc_final: 0.8823 (t0) REVERT: D 178 MET cc_start: 0.7828 (ppp) cc_final: 0.7518 (ppp) REVERT: D 190 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9038 (mtmm) REVERT: E 177 MET cc_start: 0.8822 (pmm) cc_final: 0.8241 (pmm) REVERT: E 180 MET cc_start: 0.7928 (ppp) cc_final: 0.7724 (ppp) REVERT: F 35 ASN cc_start: 0.6951 (t0) cc_final: 0.6244 (m-40) REVERT: F 83 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9343 (tt) REVERT: F 87 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: F 128 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8989 (ttpp) REVERT: F 210 MET cc_start: 0.8606 (ppp) cc_final: 0.8312 (tmm) REVERT: I 52 LYS cc_start: 0.9489 (mtmt) cc_final: 0.9228 (mtmt) REVERT: I 72 LEU cc_start: 0.9577 (tt) cc_final: 0.9316 (mm) REVERT: G 52 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9262 (ttpp) REVERT: G 63 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9182 (tt) REVERT: H 3 ASP cc_start: 0.9052 (p0) cc_final: 0.8743 (p0) REVERT: H 4 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9168 (mp) REVERT: H 44 GLU cc_start: 0.6347 (mp0) cc_final: 0.5886 (mp0) REVERT: H 45 GLN cc_start: 0.8935 (pm20) cc_final: 0.7926 (mm-40) REVERT: H 49 PHE cc_start: 0.8946 (t80) cc_final: 0.8706 (t80) REVERT: H 52 LYS cc_start: 0.9572 (ptmt) cc_final: 0.9234 (ptpp) REVERT: J 79 MET cc_start: 0.9306 (ppp) cc_final: 0.9041 (ppp) outliers start: 49 outliers final: 26 residues processed: 357 average time/residue: 0.2073 time to fit residues: 108.1148 Evaluate side-chains 327 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049579 restraints weight = 49667.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051245 restraints weight = 27191.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052145 restraints weight = 18509.352| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11668 Z= 0.155 Angle : 0.838 14.167 15814 Z= 0.402 Chirality : 0.043 0.200 1927 Planarity : 0.004 0.065 1877 Dihedral : 5.148 45.987 1516 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 4.02 % Allowed : 27.32 % Favored : 68.66 % 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: -0.87 (0.23), residues: 1414 helix: 0.06 (0.16), residues: 1094 sheet: None (None), residues: 0 loop : -2.57 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 200 HIS 0.003 0.001 HIS F 247 PHE 0.021 0.001 PHE J 74 TYR 0.022 0.001 TYR G 13 ARG 0.003 0.001 ARG F 44 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 675) hydrogen bonds : angle 4.51416 ( 2019) covalent geometry : bond 0.00367 (11668) covalent geometry : angle 0.83840 (15814) *********************** 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 371 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 1.369 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: A 36 MET cc_start: 0.9175 (ttm) cc_final: 0.8877 (ttm) REVERT: A 50 MET cc_start: 0.9056 (tpp) cc_final: 0.8668 (tpt) REVERT: A 81 LYS cc_start: 0.8986 (tppt) cc_final: 0.8317 (tptp) REVERT: A 93 ASP cc_start: 0.9022 (m-30) cc_final: 0.8558 (p0) REVERT: A 171 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9235 (pt) REVERT: A 175 LEU cc_start: 0.9543 (tp) cc_final: 0.9211 (pp) REVERT: B 45 GLN cc_start: 0.8969 (tp40) cc_final: 0.8585 (tp-100) REVERT: B 108 ASP cc_start: 0.8800 (t0) cc_final: 0.8444 (t0) REVERT: B 111 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8959 (tt) REVERT: B 149 ASP cc_start: 0.9017 (t0) cc_final: 0.8509 (t0) REVERT: B 156 TYR cc_start: 0.8130 (m-10) cc_final: 0.7519 (m-80) REVERT: B 179 MET cc_start: 0.8903 (mmm) cc_final: 0.8320 (mmm) REVERT: C 48 SER cc_start: 0.8793 (t) cc_final: 0.8419 (p) REVERT: C 50 MET cc_start: 0.8632 (tpt) cc_final: 0.8302 (tpt) REVERT: C 135 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7737 (pp) REVERT: C 169 SER cc_start: 0.9720 (t) cc_final: 0.9469 (p) REVERT: C 179 MET cc_start: 0.8709 (mmm) cc_final: 0.8294 (mmm) REVERT: C 198 ASP cc_start: 0.8526 (t0) cc_final: 0.8169 (t0) REVERT: D 50 MET cc_start: 0.8820 (tmm) cc_final: 0.8581 (tmm) REVERT: D 64 MET cc_start: 0.9377 (mmp) cc_final: 0.9175 (mmp) REVERT: D 142 TYR cc_start: 0.8424 (t80) cc_final: 0.8065 (t80) REVERT: D 146 GLU cc_start: 0.9510 (OUTLIER) cc_final: 0.9176 (mt-10) REVERT: D 149 ASP cc_start: 0.9303 (t0) cc_final: 0.8848 (t0) REVERT: D 179 MET cc_start: 0.8342 (mmm) cc_final: 0.7897 (mmm) REVERT: D 190 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9049 (mtmm) REVERT: E 39 ASN cc_start: 0.9055 (m110) cc_final: 0.8769 (m110) REVERT: E 177 MET cc_start: 0.8858 (pmm) cc_final: 0.8209 (pmm) REVERT: E 205 LYS cc_start: 0.9267 (tptm) cc_final: 0.8945 (tptt) REVERT: F 35 ASN cc_start: 0.6810 (t0) cc_final: 0.6100 (m-40) REVERT: F 128 LYS cc_start: 0.9249 (ttpp) cc_final: 0.8838 (ttpp) REVERT: F 248 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8956 (mmtm) REVERT: I 13 TYR cc_start: 0.8525 (t80) cc_final: 0.8174 (m-80) REVERT: I 52 LYS cc_start: 0.9473 (mtmt) cc_final: 0.9221 (mtmt) REVERT: G 52 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9249 (ttpp) REVERT: G 63 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9209 (tt) REVERT: H 3 ASP cc_start: 0.9051 (p0) cc_final: 0.8767 (p0) REVERT: H 49 PHE cc_start: 0.9037 (t80) cc_final: 0.8769 (t80) REVERT: H 52 LYS cc_start: 0.9543 (ptmt) cc_final: 0.9210 (ptpp) REVERT: J 67 TYR cc_start: 0.9014 (m-80) cc_final: 0.8781 (m-80) REVERT: J 79 MET cc_start: 0.9351 (ppp) cc_final: 0.9065 (ppp) outliers start: 51 outliers final: 29 residues processed: 356 average time/residue: 0.1877 time to fit residues: 100.4937 Evaluate side-chains 333 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 70 optimal weight: 0.0670 chunk 132 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN H 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050434 restraints weight = 49771.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052115 restraints weight = 27020.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053184 restraints weight = 18291.626| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11668 Z= 0.148 Angle : 0.886 12.320 15814 Z= 0.420 Chirality : 0.044 0.210 1927 Planarity : 0.005 0.070 1877 Dihedral : 5.125 45.632 1516 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 3.31 % Allowed : 29.06 % Favored : 67.64 % 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: 0.04 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -2.63 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 200 HIS 0.003 0.001 HIS F 70 PHE 0.017 0.001 PHE A 30 TYR 0.038 0.001 TYR I 13 ARG 0.002 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 675) hydrogen bonds : angle 4.46923 ( 2019) covalent geometry : bond 0.00350 (11668) covalent geometry : angle 0.88565 (15814) *********************** 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 363 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 1.222 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: A 36 MET cc_start: 0.9150 (ttm) cc_final: 0.8867 (ttm) REVERT: A 50 MET cc_start: 0.8979 (tpp) cc_final: 0.8573 (tpt) REVERT: A 69 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 81 LYS cc_start: 0.9058 (tppt) cc_final: 0.8455 (tptp) REVERT: A 175 LEU cc_start: 0.9541 (tp) cc_final: 0.9237 (pp) REVERT: A 178 MET cc_start: 0.8488 (pmm) cc_final: 0.8222 (pmm) REVERT: B 108 ASP cc_start: 0.8763 (t0) cc_final: 0.8399 (t0) REVERT: B 111 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8961 (tt) REVERT: B 149 ASP cc_start: 0.8983 (t0) cc_final: 0.8442 (t0) REVERT: B 179 MET cc_start: 0.8758 (mmm) cc_final: 0.8161 (mmm) REVERT: B 180 MET cc_start: 0.9078 (ppp) cc_final: 0.8410 (ppp) REVERT: C 48 SER cc_start: 0.8710 (t) cc_final: 0.8316 (p) REVERT: C 50 MET cc_start: 0.8608 (tpt) cc_final: 0.8278 (tpt) REVERT: C 135 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7731 (pp) REVERT: C 158 TYR cc_start: 0.9029 (t80) cc_final: 0.8710 (t80) REVERT: C 179 MET cc_start: 0.8730 (mmm) cc_final: 0.8362 (mmm) REVERT: C 198 ASP cc_start: 0.8528 (t0) cc_final: 0.8164 (t0) REVERT: D 142 TYR cc_start: 0.8351 (t80) cc_final: 0.7978 (t80) REVERT: D 146 GLU cc_start: 0.9516 (OUTLIER) cc_final: 0.9224 (mt-10) REVERT: D 149 ASP cc_start: 0.9309 (t0) cc_final: 0.8808 (t0) REVERT: D 190 LYS cc_start: 0.9313 (mtmt) cc_final: 0.9052 (mtmm) REVERT: E 39 ASN cc_start: 0.9034 (m110) cc_final: 0.8760 (m-40) REVERT: E 177 MET cc_start: 0.8720 (pmm) cc_final: 0.8264 (pmm) REVERT: E 205 LYS cc_start: 0.9095 (tptm) cc_final: 0.8887 (tptp) REVERT: E 213 ASN cc_start: 0.9131 (p0) cc_final: 0.8918 (t0) REVERT: F 22 PHE cc_start: 0.8766 (m-80) cc_final: 0.8393 (m-80) REVERT: F 35 ASN cc_start: 0.6820 (t0) cc_final: 0.6159 (m-40) REVERT: F 87 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: F 248 LYS cc_start: 0.9343 (mmtt) cc_final: 0.9033 (mmtm) REVERT: I 19 SER cc_start: 0.9545 (t) cc_final: 0.9170 (p) REVERT: G 52 LYS cc_start: 0.9543 (mtmt) cc_final: 0.9270 (ttpp) REVERT: G 63 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9218 (tt) REVERT: H 3 ASP cc_start: 0.9037 (p0) cc_final: 0.8791 (p0) REVERT: H 44 GLU cc_start: 0.6466 (mp0) cc_final: 0.5897 (mp0) REVERT: H 45 GLN cc_start: 0.9074 (pm20) cc_final: 0.8122 (mm-40) REVERT: H 52 LYS cc_start: 0.9565 (ptmt) cc_final: 0.9349 (ptpp) REVERT: J 67 TYR cc_start: 0.9025 (m-80) cc_final: 0.8777 (m-80) outliers start: 42 outliers final: 31 residues processed: 349 average time/residue: 0.2041 time to fit residues: 107.3644 Evaluate side-chains 324 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050614 restraints weight = 49606.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052297 restraints weight = 26955.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053469 restraints weight = 18353.239| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6156 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= 0.154 Angle : 0.924 17.606 15814 Z= 0.433 Chirality : 0.045 0.237 1927 Planarity : 0.005 0.073 1877 Dihedral : 5.117 45.971 1516 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 3.54 % Allowed : 30.31 % Favored : 66.14 % 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: -0.77 (0.23), residues: 1414 helix: 0.18 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.67 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 PHE 0.042 0.001 PHE H 49 TYR 0.038 0.002 TYR A 158 ARG 0.003 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 675) hydrogen bonds : angle 4.50741 ( 2019) covalent geometry : bond 0.00364 (11668) covalent geometry : angle 0.92363 (15814) *********************** 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 349 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 1.518 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: A 26 CYS cc_start: 0.7475 (t) cc_final: 0.7135 (t) REVERT: A 49 ASN cc_start: 0.8708 (t0) cc_final: 0.8468 (t0) REVERT: A 50 MET cc_start: 0.8945 (tpp) cc_final: 0.8706 (tpp) REVERT: A 81 LYS cc_start: 0.9102 (tppt) cc_final: 0.8541 (tptp) REVERT: A 175 LEU cc_start: 0.9551 (tp) cc_final: 0.9196 (pp) REVERT: B 108 ASP cc_start: 0.8777 (t0) cc_final: 0.8402 (t0) REVERT: B 111 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8944 (tt) REVERT: B 149 ASP cc_start: 0.8988 (t0) cc_final: 0.8463 (t0) REVERT: B 179 MET cc_start: 0.8669 (mmm) cc_final: 0.7861 (mmm) REVERT: B 180 MET cc_start: 0.9059 (ppp) cc_final: 0.8281 (ppp) REVERT: C 48 SER cc_start: 0.8747 (t) cc_final: 0.8368 (p) REVERT: C 50 MET cc_start: 0.8617 (tpt) cc_final: 0.8311 (tpt) REVERT: C 135 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7717 (pp) REVERT: C 158 TYR cc_start: 0.9023 (t80) cc_final: 0.8703 (t80) REVERT: C 198 ASP cc_start: 0.8568 (t0) cc_final: 0.8225 (t0) REVERT: D 64 MET cc_start: 0.9264 (mmp) cc_final: 0.9027 (mmm) REVERT: D 142 TYR cc_start: 0.8412 (t80) cc_final: 0.8006 (t80) REVERT: D 146 GLU cc_start: 0.9533 (OUTLIER) cc_final: 0.9217 (mt-10) REVERT: D 149 ASP cc_start: 0.9297 (t0) cc_final: 0.8786 (t0) REVERT: E 15 THR cc_start: 0.9151 (m) cc_final: 0.8899 (p) REVERT: E 39 ASN cc_start: 0.9016 (m110) cc_final: 0.8777 (m-40) REVERT: E 177 MET cc_start: 0.8681 (pmm) cc_final: 0.8280 (pmm) REVERT: E 190 LYS cc_start: 0.9448 (mtmt) cc_final: 0.8694 (mtmm) REVERT: E 205 LYS cc_start: 0.9146 (tptm) cc_final: 0.8862 (tptp) REVERT: F 22 PHE cc_start: 0.8750 (m-80) cc_final: 0.8378 (m-80) REVERT: F 35 ASN cc_start: 0.6844 (t0) cc_final: 0.6241 (m-40) REVERT: F 87 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: F 128 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8927 (ttpp) REVERT: F 220 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8813 (tmmt) REVERT: F 248 LYS cc_start: 0.9357 (mmtt) cc_final: 0.9095 (mmtp) REVERT: I 19 SER cc_start: 0.9530 (t) cc_final: 0.9163 (p) REVERT: G 63 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9228 (tt) REVERT: H 3 ASP cc_start: 0.9059 (p0) cc_final: 0.8829 (p0) REVERT: H 52 LYS cc_start: 0.9589 (ptmt) cc_final: 0.9369 (ptpp) REVERT: J 67 TYR cc_start: 0.9030 (m-80) cc_final: 0.8799 (m-80) outliers start: 45 outliers final: 31 residues processed: 338 average time/residue: 0.2650 time to fit residues: 133.2150 Evaluate side-chains 320 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN ** H 41 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 = 0.3317 r_free = 0.3317 target = 0.066403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050669 restraints weight = 49827.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052287 restraints weight = 27279.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053352 restraints weight = 18665.435| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11668 Z= 0.157 Angle : 0.939 16.073 15814 Z= 0.440 Chirality : 0.045 0.260 1927 Planarity : 0.005 0.077 1877 Dihedral : 5.123 45.905 1516 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 3.62 % Allowed : 30.31 % Favored : 66.06 % 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: -0.71 (0.23), residues: 1414 helix: 0.23 (0.16), residues: 1087 sheet: None (None), residues: 0 loop : -2.68 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 PHE 0.025 0.001 PHE J 74 TYR 0.041 0.002 TYR A 142 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 675) hydrogen bonds : angle 4.51916 ( 2019) covalent geometry : bond 0.00376 (11668) covalent geometry : angle 0.93878 (15814) *********************** 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 350 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 1.421 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: A 36 MET cc_start: 0.9200 (ttm) cc_final: 0.8949 (ttm) REVERT: A 49 ASN cc_start: 0.8663 (t0) cc_final: 0.8414 (t0) REVERT: A 50 MET cc_start: 0.8924 (tpp) cc_final: 0.8650 (tpp) REVERT: A 81 LYS cc_start: 0.9170 (tppt) cc_final: 0.8610 (tptp) REVERT: A 90 ARG cc_start: 0.9228 (ptp-110) cc_final: 0.8923 (ptp90) REVERT: A 158 TYR cc_start: 0.8892 (t80) cc_final: 0.8678 (t80) REVERT: B 108 ASP cc_start: 0.8765 (t0) cc_final: 0.8406 (t0) REVERT: B 110 GLU cc_start: 0.8825 (pp20) cc_final: 0.8622 (pp20) REVERT: B 111 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 149 ASP cc_start: 0.9016 (t0) cc_final: 0.8494 (t0) REVERT: B 180 MET cc_start: 0.8988 (ppp) cc_final: 0.8232 (ppp) REVERT: C 48 SER cc_start: 0.8718 (t) cc_final: 0.8299 (p) REVERT: C 50 MET cc_start: 0.8621 (tpt) cc_final: 0.8307 (tpt) REVERT: C 135 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7726 (pp) REVERT: C 158 TYR cc_start: 0.9035 (t80) cc_final: 0.8646 (t80) REVERT: C 198 ASP cc_start: 0.8608 (t0) cc_final: 0.8232 (t0) REVERT: D 142 TYR cc_start: 0.8435 (t80) cc_final: 0.8069 (t80) REVERT: D 146 GLU cc_start: 0.9551 (OUTLIER) cc_final: 0.9262 (mt-10) REVERT: D 149 ASP cc_start: 0.9313 (t0) cc_final: 0.8941 (t0) REVERT: D 190 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8927 (mtmm) REVERT: E 15 THR cc_start: 0.9147 (m) cc_final: 0.8896 (p) REVERT: E 39 ASN cc_start: 0.9048 (m110) cc_final: 0.8756 (m-40) REVERT: E 177 MET cc_start: 0.8617 (pmm) cc_final: 0.8304 (pmm) REVERT: E 190 LYS cc_start: 0.9443 (mtmt) cc_final: 0.8696 (mtmm) REVERT: E 205 LYS cc_start: 0.9153 (tptm) cc_final: 0.8885 (tptp) REVERT: F 22 PHE cc_start: 0.8770 (m-80) cc_final: 0.8384 (m-80) REVERT: F 35 ASN cc_start: 0.7021 (t0) cc_final: 0.6357 (m-40) REVERT: F 87 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8905 (m-80) REVERT: F 248 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9014 (mmtm) REVERT: I 19 SER cc_start: 0.9524 (t) cc_final: 0.9171 (p) REVERT: I 52 LYS cc_start: 0.9462 (mtmt) cc_final: 0.9213 (mtmt) REVERT: G 59 SER cc_start: 0.9501 (t) cc_final: 0.9233 (p) REVERT: G 63 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9218 (tt) REVERT: H 3 ASP cc_start: 0.9088 (p0) cc_final: 0.8859 (p0) REVERT: H 45 GLN cc_start: 0.9098 (pm20) cc_final: 0.8687 (mp10) REVERT: H 77 GLU cc_start: 0.9184 (pt0) cc_final: 0.8818 (pt0) REVERT: J 67 TYR cc_start: 0.8996 (m-80) cc_final: 0.8777 (m-80) outliers start: 46 outliers final: 34 residues processed: 335 average time/residue: 0.2544 time to fit residues: 127.2941 Evaluate side-chains 336 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 HIS ** H 41 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 = 0.3318 r_free = 0.3318 target = 0.066466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050759 restraints weight = 49384.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052363 restraints weight = 27185.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053552 restraints weight = 18767.417| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11668 Z= 0.159 Angle : 0.976 15.736 15814 Z= 0.449 Chirality : 0.046 0.289 1927 Planarity : 0.005 0.079 1877 Dihedral : 5.091 45.929 1516 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 3.15 % Allowed : 31.18 % Favored : 65.67 % 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: -0.63 (0.23), residues: 1414 helix: 0.29 (0.16), residues: 1086 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 200 HIS 0.004 0.001 HIS F 70 PHE 0.034 0.001 PHE H 49 TYR 0.026 0.001 TYR A 142 ARG 0.002 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 675) hydrogen bonds : angle 4.52716 ( 2019) covalent geometry : bond 0.00378 (11668) covalent geometry : angle 0.97559 (15814) ********************** 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 343 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 2.156 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: A 36 MET cc_start: 0.9198 (ttm) cc_final: 0.8898 (ttm) REVERT: A 49 ASN cc_start: 0.8660 (t0) cc_final: 0.8408 (t0) REVERT: A 50 MET cc_start: 0.8887 (tpp) cc_final: 0.8605 (tpp) REVERT: A 81 LYS cc_start: 0.9242 (tppt) cc_final: 0.8707 (tptp) REVERT: B 108 ASP cc_start: 0.8761 (t0) cc_final: 0.8405 (t0) REVERT: B 110 GLU cc_start: 0.8897 (pp20) cc_final: 0.8687 (pp20) REVERT: B 111 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8957 (tt) REVERT: B 149 ASP cc_start: 0.9017 (t0) cc_final: 0.8485 (t0) REVERT: B 179 MET cc_start: 0.8387 (mmm) cc_final: 0.8057 (mmm) REVERT: B 180 MET cc_start: 0.8936 (ppp) cc_final: 0.8186 (ppp) REVERT: C 31 SER cc_start: 0.9168 (t) cc_final: 0.8780 (p) REVERT: C 48 SER cc_start: 0.8734 (t) cc_final: 0.8282 (p) REVERT: C 50 MET cc_start: 0.8660 (tpt) cc_final: 0.8347 (tpt) REVERT: C 135 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7721 (pp) REVERT: C 158 TYR cc_start: 0.9051 (t80) cc_final: 0.8664 (t80) REVERT: C 198 ASP cc_start: 0.8632 (t0) cc_final: 0.8235 (t70) REVERT: D 142 TYR cc_start: 0.8439 (t80) cc_final: 0.8038 (t80) REVERT: D 146 GLU cc_start: 0.9549 (OUTLIER) cc_final: 0.9243 (mt-10) REVERT: D 149 ASP cc_start: 0.9390 (t0) cc_final: 0.8929 (t0) REVERT: D 179 MET cc_start: 0.8282 (tpp) cc_final: 0.7819 (tpp) REVERT: D 190 LYS cc_start: 0.9279 (mtmt) cc_final: 0.8964 (mtmm) REVERT: E 15 THR cc_start: 0.9155 (m) cc_final: 0.8905 (p) REVERT: E 39 ASN cc_start: 0.9051 (m110) cc_final: 0.8729 (m-40) REVERT: E 177 MET cc_start: 0.8602 (pmm) cc_final: 0.8328 (pmm) REVERT: E 190 LYS cc_start: 0.9433 (mtmt) cc_final: 0.8674 (mtmm) REVERT: E 205 LYS cc_start: 0.9158 (tptm) cc_final: 0.8922 (tptp) REVERT: F 22 PHE cc_start: 0.8735 (m-80) cc_final: 0.8373 (m-80) REVERT: F 35 ASN cc_start: 0.7006 (t0) cc_final: 0.6401 (m-40) REVERT: F 128 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8876 (ttpp) REVERT: F 248 LYS cc_start: 0.9413 (mmtt) cc_final: 0.9126 (mmtp) REVERT: I 19 SER cc_start: 0.9481 (t) cc_final: 0.9119 (p) REVERT: I 52 LYS cc_start: 0.9503 (mtmt) cc_final: 0.9213 (mtmt) REVERT: G 59 SER cc_start: 0.9516 (t) cc_final: 0.9203 (p) REVERT: G 63 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9233 (tt) REVERT: G 79 MET cc_start: 0.9551 (mmm) cc_final: 0.8967 (mmm) REVERT: H 3 ASP cc_start: 0.9091 (p0) cc_final: 0.8863 (p0) REVERT: H 37 GLN cc_start: 0.9002 (mt0) cc_final: 0.7587 (tp40) REVERT: H 45 GLN cc_start: 0.9119 (pm20) cc_final: 0.8891 (mt0) REVERT: H 77 GLU cc_start: 0.9174 (pt0) cc_final: 0.8791 (pt0) outliers start: 40 outliers final: 35 residues processed: 328 average time/residue: 0.2496 time to fit residues: 122.4145 Evaluate side-chains 327 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051444 restraints weight = 49311.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053083 restraints weight = 27256.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054122 restraints weight = 18725.494| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11668 Z= 0.156 Angle : 0.972 15.578 15814 Z= 0.448 Chirality : 0.046 0.353 1927 Planarity : 0.005 0.080 1877 Dihedral : 5.091 46.137 1516 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 3.07 % Allowed : 31.26 % Favored : 65.67 % 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: -0.59 (0.23), residues: 1414 helix: 0.32 (0.16), residues: 1089 sheet: None (None), residues: 0 loop : -2.68 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 200 HIS 0.001 0.000 HIS D 106 PHE 0.029 0.001 PHE H 49 TYR 0.045 0.002 TYR A 158 ARG 0.002 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 675) hydrogen bonds : angle 4.52860 ( 2019) covalent geometry : bond 0.00371 (11668) covalent geometry : angle 0.97248 (15814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4673.51 seconds wall clock time: 85 minutes 51.94 seconds (5151.94 seconds total)