Starting phenix.real_space_refine on Thu Mar 5 06:31:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sfx_10162/03_2026/6sfx_10162.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.009 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 98 5.16 5 C 12707 2.51 5 N 3444 2.21 5 O 3947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "D" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "E" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "F" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "G" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "H" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1470 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "I" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1465 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "K" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1445 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "L" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1483 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Chain: "M" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1483 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Chain: "N" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1490 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 4.77, per 1000 atoms: 0.24 Number of scatterers: 20196 At special positions: 0 Unit cell: (111.18, 110.09, 115.54, 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 98 16.00 O 3947 8.00 N 3444 7.00 C 12707 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 723.4 milliseconds 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 52.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.652A pdb=" N ILE A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 56 removed outlier: 4.192A pdb=" N GLU A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 4.502A pdb=" N THR A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 82 " --> pdb=" O HIS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.221A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 107 No H-bonds generated for 'chain 'A' and resid 106 through 107' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.590A pdb=" N GLU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 176 through 183 removed outlier: 3.688A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.666A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.663A pdb=" N ASP B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.879A pdb=" N ASP B 75 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 132 through 159 removed outlier: 3.703A pdb=" N ILE B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.538A pdb=" N ASP B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.758A pdb=" N THR C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.877A pdb=" N ASP C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 84 removed outlier: 4.075A pdb=" N ILE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.516A pdb=" N THR C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 159 removed outlier: 3.691A pdb=" N ILE C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.696A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.603A pdb=" N ASP C 182 " --> pdb=" O ASN C 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.563A pdb=" N LEU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.824A pdb=" N GLN D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.877A pdb=" N ILE D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.599A pdb=" N ALA D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 159 removed outlier: 3.918A pdb=" N ALA D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 177 through 184 removed outlier: 4.087A pdb=" N ASP D 182 " --> pdb=" O ASN D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 38 through 56 removed outlier: 3.927A pdb=" N ASP E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.845A pdb=" N THR E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 107 removed outlier: 3.670A pdb=" N THR E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.517A pdb=" N GLU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.710A pdb=" N ILE F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 56 removed outlier: 3.575A pdb=" N GLN F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.567A pdb=" N GLY F 74 " --> pdb=" O HIS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.597A pdb=" N TYR F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 132 through 158 removed outlier: 3.582A pdb=" N ASN F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 169 Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.805A pdb=" N GLN G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 24 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 56 removed outlier: 4.678A pdb=" N ASP G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.646A pdb=" N THR G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 159 removed outlier: 3.651A pdb=" N GLU G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.638A pdb=" N ASP G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 184 Processing helix chain 'H' and resid 20 through 27 Processing helix chain 'H' and resid 37 through 55 removed outlier: 4.415A pdb=" N SER H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER H 46 " --> pdb=" O ASN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 removed outlier: 4.871A pdb=" N ALA H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 133 through 159 removed outlier: 3.992A pdb=" N ILE H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR H 158 " --> pdb=" O MET H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.887A pdb=" N ILE H 165 " --> pdb=" O PRO H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 184 removed outlier: 3.906A pdb=" N ASP H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 14 Processing helix chain 'I' and resid 19 through 27 Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.662A pdb=" N SER I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP I 55 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.580A pdb=" N GLY I 74 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 105 Processing helix chain 'I' and resid 133 through 157 removed outlier: 3.525A pdb=" N LYS I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.541A pdb=" N ILE I 165 " --> pdb=" O PRO I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 19 through 27 removed outlier: 3.551A pdb=" N LEU J 24 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 55 removed outlier: 3.637A pdb=" N VAL J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER J 46 " --> pdb=" O ASN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.563A pdb=" N ALA J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 105 Processing helix chain 'J' and resid 132 through 159 Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 184 Processing helix chain 'K' and resid 20 through 27 Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.525A pdb=" N SER K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.940A pdb=" N ALA K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 107 Processing helix chain 'K' and resid 132 through 159 removed outlier: 3.973A pdb=" N ILE K 138 " --> pdb=" O THR K 134 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS K 147 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.926A pdb=" N ILE K 165 " --> pdb=" O PRO K 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 184 Processing helix chain 'K' and resid 191 through 196 Processing helix chain 'L' and resid 21 through 26 Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.557A pdb=" N ALA L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 removed outlier: 4.176A pdb=" N ALA L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 161 through 171 removed outlier: 4.312A pdb=" N ARG L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 184 Processing helix chain 'M' and resid 19 through 27 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.938A pdb=" N SER M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER M 46 " --> pdb=" O ASN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.711A pdb=" N GLY M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 107 removed outlier: 3.698A pdb=" N PHE M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 159 removed outlier: 3.860A pdb=" N ALA M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR M 158 " --> pdb=" O MET M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.529A pdb=" N ARG M 167 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.611A pdb=" N ALA M 180 " --> pdb=" O THR M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 11 Processing helix chain 'N' and resid 20 through 27 Processing helix chain 'N' and resid 37 through 54 removed outlier: 3.766A pdb=" N SER N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 99 through 106 removed outlier: 3.699A pdb=" N LEU N 104 " --> pdb=" O GLY N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 159 removed outlier: 3.902A pdb=" N GLU N 156 " --> pdb=" O THR N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 169 Processing helix chain 'N' and resid 177 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.624A pdb=" N VAL A 31 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 65 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 33 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 113 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 90 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.707A pdb=" N ILE B 37 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 62 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 97 Processing sheet with id=AA7, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 129 removed outlier: 3.578A pdb=" N GLY N 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 34 removed outlier: 6.922A pdb=" N VAL C 31 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN C 65 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 33 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 60 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 91 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE C 62 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE C 113 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 90 " --> pdb=" O PHE C 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AB2, first strand: chain 'C' and resid 126 through 132 Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 37 removed outlier: 7.068A pdb=" N ILE D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER D 66 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY D 35 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY D 68 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL D 91 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE D 62 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE D 113 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL D 90 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB5, first strand: chain 'D' and resid 129 through 132 Processing sheet with id=AB6, first strand: chain 'E' and resid 30 through 34 removed outlier: 7.085A pdb=" N VAL E 31 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN E 65 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 33 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL E 91 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 62 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE E 113 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL E 90 " --> pdb=" O PHE E 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AB9, first strand: chain 'F' and resid 30 through 34 removed outlier: 5.722A pdb=" N ILE F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL F 91 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE F 62 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE F 113 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL F 90 " --> pdb=" O PHE F 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 131 Processing sheet with id=AC3, first strand: chain 'G' and resid 30 through 34 removed outlier: 6.252A pdb=" N VAL G 90 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 95 through 96 Processing sheet with id=AC5, first strand: chain 'G' and resid 127 through 132 Processing sheet with id=AC6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.419A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE H 113 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR H 90 " --> pdb=" O PHE H 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA H 114 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 95 through 96 removed outlier: 6.518A pdb=" N ALA H 96 " --> pdb=" O MET H 121 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS H 123 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.584A pdb=" N ILE I 30 " --> pdb=" O PHE I 61 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU I 62 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR I 90 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP I 188 " --> pdb=" O ARG I 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 95 through 96 Processing sheet with id=AD2, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.508A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.508A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU J 119 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY J 94 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N MET J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA J 96 " --> pdb=" O MET J 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN J 173 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.641A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE K 113 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR K 90 " --> pdb=" O PHE K 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 119 through 122 Processing sheet with id=AD6, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.426A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE L 113 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR L 90 " --> pdb=" O PHE L 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 188 " --> pdb=" O ARG L 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 95 through 96 removed outlier: 6.880A pdb=" N ALA L 96 " --> pdb=" O MET L 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.133A pdb=" N ILE M 60 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE M 91 " --> pdb=" O ILE M 60 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU M 62 " --> pdb=" O ILE M 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE M 113 " --> pdb=" O VAL M 88 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR M 90 " --> pdb=" O PHE M 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP M 188 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.512A pdb=" N TYR N 18 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.443A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU N 62 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP N 188 " --> pdb=" O ARG N 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 95 through 96 980 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3909 1.32 - 1.44: 4631 1.44 - 1.57: 11720 1.57 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 20456 Sorted by residual: bond pdb=" C SER G 114 " pdb=" N LEU G 115 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.86e-02 2.89e+03 2.76e+01 bond pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 1.331 1.381 -0.050 9.80e-03 1.04e+04 2.60e+01 bond pdb=" C ALA J 114 " pdb=" N LEU J 115 " ideal model delta sigma weight residual 1.330 1.270 0.060 1.47e-02 4.63e+03 1.64e+01 bond pdb=" N ILE K 191 " pdb=" CA ILE K 191 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" N ILE K 190 " pdb=" CA ILE K 190 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.38e+01 ... (remaining 20451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 25866 1.93 - 3.86: 1540 3.86 - 5.79: 197 5.79 - 7.72: 19 7.72 - 9.66: 2 Bond angle restraints: 27624 Sorted by residual: angle pdb=" C PRO H 125 " pdb=" CA PRO H 125 " pdb=" CB PRO H 125 " ideal model delta sigma weight residual 111.87 105.62 6.25 8.40e-01 1.42e+00 5.53e+01 angle pdb=" O ILE B 189 " pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 122.62 128.72 -6.10 1.17e+00 7.31e-01 2.71e+01 angle pdb=" CA ILE B 189 " pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 116.27 110.04 6.23 1.27e+00 6.20e-01 2.41e+01 angle pdb=" C GLN H 124 " pdb=" N PRO H 125 " pdb=" CA PRO H 125 " ideal model delta sigma weight residual 120.79 127.06 -6.27 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CA ILE G 189 " pdb=" C ILE G 189 " pdb=" O ILE G 189 " ideal model delta sigma weight residual 122.63 118.48 4.15 8.70e-01 1.32e+00 2.28e+01 ... (remaining 27619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11012 17.82 - 35.64: 1196 35.64 - 53.46: 200 53.46 - 71.28: 63 71.28 - 89.09: 40 Dihedral angle restraints: 12511 sinusoidal: 5042 harmonic: 7469 Sorted by residual: dihedral pdb=" CA GLU L 15 " pdb=" C GLU L 15 " pdb=" N ARG L 16 " pdb=" CA ARG L 16 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU C 175 " pdb=" C LEU C 175 " pdb=" N SER C 176 " pdb=" CA SER C 176 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET M 175 " pdb=" C MET M 175 " pdb=" N THR M 176 " pdb=" CA THR M 176 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 12508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2455 0.067 - 0.134: 656 0.134 - 0.202: 78 0.202 - 0.269: 12 0.269 - 0.336: 5 Chirality restraints: 3206 Sorted by residual: chirality pdb=" CA LEU H 126 " pdb=" N LEU H 126 " pdb=" C LEU H 126 " pdb=" CB LEU H 126 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB ILE K 191 " pdb=" CA ILE K 191 " pdb=" CG1 ILE K 191 " pdb=" CG2 ILE K 191 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3203 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 188 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C GLU F 188 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU F 188 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE F 189 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 188 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLU E 188 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU E 188 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE E 189 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER I 66 " -0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO I 67 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO I 67 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 67 " -0.046 5.00e-02 4.00e+02 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 3 1.43 - 2.30: 91 2.30 - 3.16: 21088 3.16 - 4.03: 54831 4.03 - 4.90: 102712 Warning: very small nonbonded interaction distances. Nonbonded interactions: 178725 Sorted by model distance: nonbonded pdb=" NZ LYS B 82 " pdb=" OE1 GLU C 191 " model vdw 0.560 3.120 nonbonded pdb=" CE LYS B 82 " pdb=" OE1 GLU C 191 " model vdw 0.929 3.440 nonbonded pdb=" NZ LYS B 82 " pdb=" CD GLU C 191 " model vdw 1.325 3.350 nonbonded pdb=" CE LYS B 82 " pdb=" CD GLU C 191 " model vdw 1.548 3.670 nonbonded pdb=" OE2 GLU B 148 " pdb=" NE ARG B 152 " model vdw 1.598 3.120 ... (remaining 178720 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'I' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'J' and (resid 1 through 8 or resid 17 through 198)) selection = chain 'K' selection = (chain 'L' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'M' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'N' and (resid 1 through 8 or resid 17 through 198)) } 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: 1.140 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.300 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.012 0.555 20457 Z= 0.665 Angle : 1.018 9.655 27624 Z= 0.599 Chirality : 0.060 0.336 3206 Planarity : 0.006 0.084 3597 Dihedral : 16.146 89.094 7701 Min Nonbonded Distance : 0.560 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 0.14 % Allowed : 0.18 % Favored : 99.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.12), residues: 2562 helix: -3.27 (0.09), residues: 1221 sheet: -2.59 (0.30), residues: 206 loop : -3.00 (0.15), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 119 TYR 0.022 0.003 TYR F 120 PHE 0.022 0.003 PHE K 50 TRP 0.049 0.005 TRP F 95 HIS 0.018 0.003 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.01181 (20456) covalent geometry : angle 1.01813 (27624) hydrogen bonds : bond 0.28141 ( 977) hydrogen bonds : angle 10.09166 ( 2865) Misc. bond : bond 0.55537 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1008 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6338 (mptt) cc_final: 0.6084 (mmtp) REVERT: A 38 ASN cc_start: 0.8388 (p0) cc_final: 0.6931 (p0) REVERT: A 75 ASP cc_start: 0.7282 (m-30) cc_final: 0.6783 (t0) REVERT: A 79 ASP cc_start: 0.7280 (m-30) cc_final: 0.6234 (m-30) REVERT: A 95 TRP cc_start: 0.7197 (t60) cc_final: 0.6864 (t60) REVERT: A 121 MET cc_start: 0.7855 (ttp) cc_final: 0.7502 (ttp) REVERT: A 167 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7513 (ttpp) REVERT: A 179 GLU cc_start: 0.7008 (mp0) cc_final: 0.6260 (mp0) REVERT: B 79 ASP cc_start: 0.7906 (m-30) cc_final: 0.7432 (m-30) REVERT: B 142 GLU cc_start: 0.7048 (mp0) cc_final: 0.6767 (mp0) REVERT: C 57 ASN cc_start: 0.7632 (m110) cc_final: 0.7404 (p0) REVERT: C 89 LYS cc_start: 0.6630 (mttt) cc_final: 0.6402 (mtpp) REVERT: D 47 LYS cc_start: 0.7869 (tttt) cc_final: 0.7589 (mttp) REVERT: D 70 HIS cc_start: 0.8211 (t-90) cc_final: 0.7766 (t70) REVERT: D 79 ASP cc_start: 0.8271 (m-30) cc_final: 0.7884 (m-30) REVERT: D 124 GLN cc_start: 0.8019 (pt0) cc_final: 0.7732 (pm20) REVERT: D 150 ILE cc_start: 0.8662 (mm) cc_final: 0.8437 (mt) REVERT: E 43 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 47 LYS cc_start: 0.7696 (tttt) cc_final: 0.6818 (mttt) REVERT: F 40 GLU cc_start: 0.8516 (pp20) cc_final: 0.7876 (mm-30) REVERT: F 61 THR cc_start: 0.9253 (m) cc_final: 0.8757 (p) REVERT: F 64 ILE cc_start: 0.9101 (mp) cc_final: 0.8862 (mm) REVERT: F 167 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7714 (mtmm) REVERT: G 27 ASP cc_start: 0.8031 (t0) cc_final: 0.7725 (m-30) REVERT: G 65 ASN cc_start: 0.7993 (t0) cc_final: 0.7615 (t0) REVERT: G 132 GLN cc_start: 0.7319 (mt0) cc_final: 0.6798 (mt0) REVERT: G 164 GLN cc_start: 0.8029 (tp40) cc_final: 0.7255 (tp-100) REVERT: G 174 TRP cc_start: 0.7533 (m-10) cc_final: 0.6548 (m100) REVERT: H 38 ASP cc_start: 0.8479 (m-30) cc_final: 0.7699 (m-30) REVERT: H 61 PHE cc_start: 0.7410 (m-80) cc_final: 0.6779 (m-80) REVERT: H 65 ASN cc_start: 0.8794 (t0) cc_final: 0.8567 (t0) REVERT: H 71 ILE cc_start: 0.8914 (mm) cc_final: 0.8487 (mm) REVERT: H 78 TYR cc_start: 0.8558 (t80) cc_final: 0.8007 (t80) REVERT: H 113 PHE cc_start: 0.7095 (m-80) cc_final: 0.6441 (m-80) REVERT: H 117 ASN cc_start: 0.7597 (m-40) cc_final: 0.7309 (m-40) REVERT: H 124 GLN cc_start: 0.7030 (pt0) cc_final: 0.6603 (pt0) REVERT: H 138 ILE cc_start: 0.8441 (mt) cc_final: 0.7687 (mm) REVERT: H 172 ASP cc_start: 0.7769 (p0) cc_final: 0.7552 (p0) REVERT: H 190 ILE cc_start: 0.9151 (mm) cc_final: 0.8691 (tp) REVERT: I 59 ASP cc_start: 0.7224 (p0) cc_final: 0.6269 (p0) REVERT: I 65 ASN cc_start: 0.8122 (t0) cc_final: 0.7159 (t0) REVERT: I 75 MET cc_start: 0.7384 (mmp) cc_final: 0.7147 (tpp) REVERT: I 82 ASN cc_start: 0.8562 (m-40) cc_final: 0.7902 (m-40) REVERT: I 116 PRO cc_start: 0.8290 (Cg_exo) cc_final: 0.8030 (Cg_endo) REVERT: I 119 GLU cc_start: 0.6069 (mm-30) cc_final: 0.5775 (mm-30) REVERT: I 132 GLN cc_start: 0.7449 (mm110) cc_final: 0.7242 (mm-40) REVERT: I 150 MET cc_start: 0.7677 (ttt) cc_final: 0.7471 (ttp) REVERT: I 160 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7630 (mp10) REVERT: I 162 TYR cc_start: 0.7187 (t80) cc_final: 0.6143 (t80) REVERT: J 1 MET cc_start: 0.0456 (ttt) cc_final: -0.0587 (tmm) REVERT: J 46 SER cc_start: 0.9281 (m) cc_final: 0.9049 (p) REVERT: J 61 PHE cc_start: 0.7919 (m-80) cc_final: 0.7705 (m-10) REVERT: J 102 PHE cc_start: 0.8475 (t80) cc_final: 0.8216 (t80) REVERT: J 123 HIS cc_start: 0.7493 (t-170) cc_final: 0.7219 (t-170) REVERT: K 23 ARG cc_start: 0.8594 (ttt90) cc_final: 0.8051 (tpt170) REVERT: K 42 ASN cc_start: 0.8633 (t0) cc_final: 0.8119 (t0) REVERT: K 72 SER cc_start: 0.7904 (p) cc_final: 0.7593 (p) REVERT: K 75 MET cc_start: 0.8283 (mmm) cc_final: 0.7834 (mmm) REVERT: K 77 ILE cc_start: 0.8888 (mm) cc_final: 0.8597 (mt) REVERT: K 79 ASP cc_start: 0.8547 (m-30) cc_final: 0.7921 (m-30) REVERT: K 99 MET cc_start: 0.6703 (tpt) cc_final: 0.6487 (tpt) REVERT: K 111 LYS cc_start: 0.8066 (mttt) cc_final: 0.7733 (mttm) REVERT: K 120 ILE cc_start: 0.8856 (mp) cc_final: 0.8194 (mt) REVERT: K 147 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8997 (pttt) REVERT: K 153 ILE cc_start: 0.9060 (mt) cc_final: 0.8839 (mt) REVERT: L 21 TYR cc_start: 0.8358 (m-10) cc_final: 0.8040 (m-10) REVERT: L 32 LEU cc_start: 0.9005 (tp) cc_final: 0.8750 (tt) REVERT: L 61 PHE cc_start: 0.6100 (m-10) cc_final: 0.4922 (m-10) REVERT: L 63 TYR cc_start: 0.6698 (m-80) cc_final: 0.5983 (m-80) REVERT: L 75 MET cc_start: 0.7827 (mmt) cc_final: 0.7623 (mmp) REVERT: L 113 PHE cc_start: 0.8552 (m-80) cc_final: 0.8351 (m-10) REVERT: L 115 LEU cc_start: 0.9002 (mt) cc_final: 0.8704 (mt) REVERT: L 135 GLU cc_start: 0.8020 (mp0) cc_final: 0.7786 (mp0) REVERT: L 150 MET cc_start: 0.7835 (mtp) cc_final: 0.7476 (mtp) REVERT: M 4 ILE cc_start: 0.7989 (mm) cc_final: 0.7429 (mm) REVERT: M 38 ASP cc_start: 0.8120 (m-30) cc_final: 0.7881 (m-30) REVERT: M 59 ASP cc_start: 0.7784 (m-30) cc_final: 0.7298 (m-30) REVERT: M 71 ILE cc_start: 0.7384 (mm) cc_final: 0.7170 (tp) REVERT: M 89 GLN cc_start: 0.7006 (tt0) cc_final: 0.6631 (tt0) REVERT: M 95 MET cc_start: 0.7923 (tpp) cc_final: 0.7719 (tpp) REVERT: M 112 ARG cc_start: 0.7286 (ptt-90) cc_final: 0.7069 (ptt180) REVERT: M 170 ASP cc_start: 0.7711 (t70) cc_final: 0.7133 (m-30) REVERT: M 171 ARG cc_start: 0.7238 (mmt180) cc_final: 0.6927 (mmt180) REVERT: M 190 ILE cc_start: 0.8132 (pt) cc_final: 0.7739 (tt) REVERT: N 1 MET cc_start: 0.3497 (mpp) cc_final: 0.2624 (tmm) REVERT: N 26 LYS cc_start: 0.7090 (tmtt) cc_final: 0.6731 (tttp) REVERT: N 78 TYR cc_start: 0.7662 (t80) cc_final: 0.7229 (t80) REVERT: N 83 PHE cc_start: 0.7161 (t80) cc_final: 0.6906 (t80) REVERT: N 95 MET cc_start: 0.6131 (mtp) cc_final: 0.5913 (mtp) REVERT: N 123 HIS cc_start: 0.8393 (t70) cc_final: 0.7298 (t70) REVERT: N 135 GLU cc_start: 0.6633 (tt0) cc_final: 0.6425 (tt0) REVERT: N 172 ASP cc_start: 0.7882 (p0) cc_final: 0.7642 (p0) REVERT: N 178 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7085 (tp40) REVERT: N 183 TYR cc_start: 0.7543 (t80) cc_final: 0.7236 (t80) outliers start: 3 outliers final: 1 residues processed: 1009 average time/residue: 0.1637 time to fit residues: 240.7732 Evaluate side-chains 697 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 696 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN B 124 GLN B 132 GLN C 19 ASN C 78 HIS D 19 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 124 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS F 123 HIS F 160 GLN G 178 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 ASN J 130 GLN K 42 ASN K 109 ASN K 142 HIS K 178 GLN L 54 GLN L 173 ASN M 65 ASN M 117 ASN M 178 GLN N 65 ASN N 82 ASN N 123 HIS N 151 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099930 restraints weight = 49412.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102854 restraints weight = 27586.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104870 restraints weight = 17320.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106301 restraints weight = 11912.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107314 restraints weight = 8762.301| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20457 Z= 0.211 Angle : 0.769 10.321 27624 Z= 0.406 Chirality : 0.048 0.217 3206 Planarity : 0.006 0.111 3597 Dihedral : 6.652 70.400 2786 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 2.91 % Allowed : 15.14 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.14), residues: 2562 helix: -1.34 (0.12), residues: 1373 sheet: -2.16 (0.32), residues: 193 loop : -2.46 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 167 TYR 0.031 0.002 TYR M 183 PHE 0.021 0.002 PHE H 113 TRP 0.025 0.003 TRP F 95 HIS 0.010 0.002 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00462 (20456) covalent geometry : angle 0.76940 (27624) hydrogen bonds : bond 0.05064 ( 977) hydrogen bonds : angle 5.78326 ( 2865) Misc. bond : bond 0.00280 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 893 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.8583 (p0) cc_final: 0.8319 (p0) REVERT: A 75 ASP cc_start: 0.7638 (m-30) cc_final: 0.6535 (t0) REVERT: A 78 HIS cc_start: 0.8258 (t-90) cc_final: 0.8046 (t70) REVERT: A 79 ASP cc_start: 0.7694 (m-30) cc_final: 0.6320 (m-30) REVERT: A 80 MET cc_start: 0.7645 (mmp) cc_final: 0.7442 (mmp) REVERT: A 83 PHE cc_start: 0.8254 (t80) cc_final: 0.8035 (t80) REVERT: A 153 LEU cc_start: 0.9074 (mp) cc_final: 0.8619 (mp) REVERT: A 167 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8150 (ptmm) REVERT: A 172 ASN cc_start: 0.8865 (m-40) cc_final: 0.8493 (m110) REVERT: B 78 HIS cc_start: 0.7978 (t70) cc_final: 0.7501 (t70) REVERT: B 124 GLN cc_start: 0.7843 (pt0) cc_final: 0.7597 (pt0) REVERT: B 139 GLU cc_start: 0.7893 (tt0) cc_final: 0.7533 (tp30) REVERT: B 146 MET cc_start: 0.8514 (ttt) cc_final: 0.8273 (ttt) REVERT: B 170 ASP cc_start: 0.8159 (p0) cc_final: 0.7925 (p0) REVERT: B 174 TRP cc_start: 0.8158 (m100) cc_final: 0.7416 (m100) REVERT: C 65 ASN cc_start: 0.7884 (t0) cc_final: 0.7557 (t0) REVERT: C 89 LYS cc_start: 0.5978 (mttt) cc_final: 0.5760 (mttm) REVERT: C 95 TRP cc_start: 0.7491 (p90) cc_final: 0.6993 (p90) REVERT: C 141 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8998 (mmmm) REVERT: C 165 ILE cc_start: 0.9115 (mt) cc_final: 0.8809 (mm) REVERT: C 172 ASN cc_start: 0.8588 (m-40) cc_final: 0.8091 (t0) REVERT: D 43 GLU cc_start: 0.8411 (tp30) cc_final: 0.8191 (tp30) REVERT: D 47 LYS cc_start: 0.7875 (tttt) cc_final: 0.7264 (ttmm) REVERT: D 79 ASP cc_start: 0.8388 (m-30) cc_final: 0.8149 (m-30) REVERT: D 124 GLN cc_start: 0.8173 (pt0) cc_final: 0.7761 (pm20) REVERT: D 146 MET cc_start: 0.7706 (tmm) cc_final: 0.7164 (ttp) REVERT: D 149 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7210 (tmm-80) REVERT: D 153 LEU cc_start: 0.8621 (mt) cc_final: 0.8377 (mp) REVERT: E 43 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6851 (tm-30) REVERT: E 47 LYS cc_start: 0.7719 (tttt) cc_final: 0.6683 (tttt) REVERT: E 129 VAL cc_start: 0.8991 (p) cc_final: 0.8774 (t) REVERT: E 153 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8161 (mt) REVERT: E 168 ASP cc_start: 0.7178 (m-30) cc_final: 0.6829 (m-30) REVERT: E 186 VAL cc_start: 0.7676 (t) cc_final: 0.7461 (t) REVERT: F 79 ASP cc_start: 0.8063 (m-30) cc_final: 0.7756 (m-30) REVERT: F 153 LEU cc_start: 0.8591 (mt) cc_final: 0.8029 (mt) REVERT: F 164 GLN cc_start: 0.8528 (tt0) cc_final: 0.8323 (pt0) REVERT: G 80 MET cc_start: 0.7982 (mmm) cc_final: 0.7573 (ttm) REVERT: G 121 MET cc_start: 0.7025 (ttt) cc_final: 0.6654 (ttt) REVERT: G 148 GLU cc_start: 0.7440 (pp20) cc_final: 0.7040 (pp20) REVERT: G 164 GLN cc_start: 0.7872 (tp40) cc_final: 0.7320 (tp-100) REVERT: G 174 TRP cc_start: 0.7645 (m100) cc_final: 0.7071 (m100) REVERT: H 78 TYR cc_start: 0.8554 (t80) cc_final: 0.8006 (t80) REVERT: H 87 ASP cc_start: 0.7188 (t70) cc_final: 0.6783 (t70) REVERT: H 138 ILE cc_start: 0.8784 (mt) cc_final: 0.8569 (mm) REVERT: H 170 ASP cc_start: 0.8202 (t0) cc_final: 0.7971 (t0) REVERT: I 59 ASP cc_start: 0.6366 (p0) cc_final: 0.6087 (p0) REVERT: I 65 ASN cc_start: 0.8241 (t0) cc_final: 0.7588 (t0) REVERT: I 81 MET cc_start: 0.7102 (tmm) cc_final: 0.6856 (tmm) REVERT: I 82 ASN cc_start: 0.8378 (m-40) cc_final: 0.7947 (m-40) REVERT: I 102 PHE cc_start: 0.8809 (t80) cc_final: 0.8595 (t80) REVERT: I 111 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7610 (mmtm) REVERT: I 119 GLU cc_start: 0.5696 (mm-30) cc_final: 0.5226 (mm-30) REVERT: I 124 GLN cc_start: 0.8559 (pt0) cc_final: 0.8321 (pm20) REVERT: I 151 ASN cc_start: 0.8590 (m-40) cc_final: 0.8387 (m110) REVERT: I 160 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7529 (mp10) REVERT: I 162 TYR cc_start: 0.7512 (t80) cc_final: 0.7210 (t80) REVERT: I 185 LEU cc_start: 0.8221 (mt) cc_final: 0.7965 (mt) REVERT: J 1 MET cc_start: 0.2862 (ttt) cc_final: 0.2130 (ttm) REVERT: J 81 MET cc_start: 0.7478 (mtm) cc_final: 0.7239 (mtt) REVERT: J 183 TYR cc_start: 0.7933 (t80) cc_final: 0.7484 (t80) REVERT: K 18 TYR cc_start: 0.6386 (p90) cc_final: 0.5818 (p90) REVERT: K 26 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8071 (tttt) REVERT: K 42 ASN cc_start: 0.8579 (t0) cc_final: 0.8038 (t0) REVERT: K 65 ASN cc_start: 0.7587 (t0) cc_final: 0.7295 (t0) REVERT: K 79 ASP cc_start: 0.8445 (m-30) cc_final: 0.7982 (m-30) REVERT: K 95 MET cc_start: 0.8036 (ttp) cc_final: 0.7755 (ttm) REVERT: K 112 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6667 (mtt90) REVERT: K 137 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7821 (tm-30) REVERT: K 171 ARG cc_start: 0.7368 (tpp-160) cc_final: 0.7139 (mmp80) REVERT: L 21 TYR cc_start: 0.8669 (m-10) cc_final: 0.8289 (m-10) REVERT: L 32 LEU cc_start: 0.8956 (tp) cc_final: 0.8627 (tt) REVERT: L 63 TYR cc_start: 0.7536 (m-80) cc_final: 0.7297 (m-80) REVERT: L 78 TYR cc_start: 0.8405 (t80) cc_final: 0.7941 (t80) REVERT: L 79 ASP cc_start: 0.8257 (m-30) cc_final: 0.8049 (m-30) REVERT: L 115 LEU cc_start: 0.9135 (mt) cc_final: 0.8689 (mt) REVERT: L 117 ASN cc_start: 0.8723 (m-40) cc_final: 0.8334 (m110) REVERT: L 149 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: L 150 MET cc_start: 0.7975 (mtp) cc_final: 0.7630 (mtp) REVERT: L 172 ASP cc_start: 0.7940 (p0) cc_final: 0.7614 (p0) REVERT: M 23 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7301 (tpm170) REVERT: M 42 ASN cc_start: 0.8913 (m-40) cc_final: 0.8377 (m110) REVERT: M 71 ILE cc_start: 0.7723 (mm) cc_final: 0.7450 (tp) REVERT: M 79 ASP cc_start: 0.8424 (m-30) cc_final: 0.7950 (m-30) REVERT: M 119 GLU cc_start: 0.7319 (mp0) cc_final: 0.6917 (mp0) REVERT: M 135 GLU cc_start: 0.8434 (mp0) cc_final: 0.7930 (mp0) REVERT: M 163 GLU cc_start: 0.8599 (mp0) cc_final: 0.8276 (pm20) REVERT: M 167 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.7709 (ttp-110) REVERT: M 170 ASP cc_start: 0.8451 (t70) cc_final: 0.7891 (m-30) REVERT: M 176 THR cc_start: 0.7356 (p) cc_final: 0.6463 (p) REVERT: M 190 ILE cc_start: 0.8023 (pt) cc_final: 0.7622 (tt) REVERT: N 1 MET cc_start: 0.3222 (mpp) cc_final: 0.1967 (tmm) REVERT: N 23 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7818 (mmm160) REVERT: N 26 LYS cc_start: 0.7996 (tttt) cc_final: 0.7247 (tttt) REVERT: N 28 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7829 (mtp85) REVERT: N 55 ASP cc_start: 0.7389 (t0) cc_final: 0.7087 (t0) REVERT: N 83 PHE cc_start: 0.7254 (t80) cc_final: 0.6833 (t80) REVERT: N 115 LEU cc_start: 0.8887 (mt) cc_final: 0.8665 (mp) REVERT: N 123 HIS cc_start: 0.7996 (t-170) cc_final: 0.7586 (t-170) REVERT: N 137 GLU cc_start: 0.8210 (tp30) cc_final: 0.7990 (tm-30) REVERT: N 150 MET cc_start: 0.8625 (tpp) cc_final: 0.8154 (tpp) REVERT: N 157 LYS cc_start: 0.8448 (mptt) cc_final: 0.8064 (mptt) REVERT: N 172 ASP cc_start: 0.7868 (p0) cc_final: 0.7593 (p0) REVERT: N 181 LYS cc_start: 0.8991 (tttm) cc_final: 0.8704 (ttmt) outliers start: 63 outliers final: 27 residues processed: 915 average time/residue: 0.1582 time to fit residues: 215.5397 Evaluate side-chains 754 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 724 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 211 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 124 GLN H 39 ASN H 117 ASN H 160 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN K 39 ASN K 82 ASN L 89 GLN M 65 ASN N 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096405 restraints weight = 49970.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099322 restraints weight = 27865.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101367 restraints weight = 17583.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102775 restraints weight = 12114.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103649 restraints weight = 8982.743| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20457 Z= 0.215 Angle : 0.740 9.249 27624 Z= 0.388 Chirality : 0.048 0.319 3206 Planarity : 0.005 0.064 3597 Dihedral : 6.321 88.280 2784 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 3.60 % Allowed : 21.50 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.15), residues: 2562 helix: -0.58 (0.13), residues: 1375 sheet: -1.49 (0.31), residues: 220 loop : -2.12 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 141 TYR 0.031 0.002 TYR E 104 PHE 0.025 0.002 PHE L 174 TRP 0.026 0.003 TRP A 95 HIS 0.014 0.002 HIS K 142 Details of bonding type rmsd covalent geometry : bond 0.00475 (20456) covalent geometry : angle 0.73984 (27624) hydrogen bonds : bond 0.04051 ( 977) hydrogen bonds : angle 5.28165 ( 2865) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 819 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.8820 (p0) cc_final: 0.8568 (p0) REVERT: A 39 GLN cc_start: 0.7475 (mt0) cc_final: 0.7188 (mt0) REVERT: A 75 ASP cc_start: 0.7570 (m-30) cc_final: 0.6610 (t0) REVERT: A 78 HIS cc_start: 0.8472 (t-90) cc_final: 0.8004 (t70) REVERT: A 79 ASP cc_start: 0.7803 (m-30) cc_final: 0.6544 (m-30) REVERT: A 153 LEU cc_start: 0.9267 (mp) cc_final: 0.8984 (mp) REVERT: B 78 HIS cc_start: 0.8029 (t70) cc_final: 0.7598 (t70) REVERT: B 121 MET cc_start: 0.8140 (tmm) cc_final: 0.7405 (tpp) REVERT: B 135 GLU cc_start: 0.8106 (tt0) cc_final: 0.7835 (tm-30) REVERT: B 139 GLU cc_start: 0.7953 (tt0) cc_final: 0.7692 (tp30) REVERT: B 151 ASN cc_start: 0.9203 (m110) cc_final: 0.8991 (m110) REVERT: C 39 GLN cc_start: 0.8191 (mt0) cc_final: 0.7838 (mt0) REVERT: C 89 LYS cc_start: 0.6021 (mttt) cc_final: 0.5777 (mttm) REVERT: C 165 ILE cc_start: 0.9164 (mt) cc_final: 0.8911 (mm) REVERT: D 40 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7994 (tm-30) REVERT: D 47 LYS cc_start: 0.8106 (tttt) cc_final: 0.7419 (ttmm) REVERT: D 79 ASP cc_start: 0.8527 (m-30) cc_final: 0.8255 (m-30) REVERT: D 143 ILE cc_start: 0.9576 (mt) cc_final: 0.9358 (tp) REVERT: D 146 MET cc_start: 0.8116 (tmm) cc_final: 0.7202 (tmm) REVERT: D 174 TRP cc_start: 0.8341 (m100) cc_final: 0.7590 (m100) REVERT: E 43 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 47 LYS cc_start: 0.7509 (tttt) cc_final: 0.6506 (tttt) REVERT: E 124 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: E 153 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 47 LYS cc_start: 0.7596 (tttt) cc_final: 0.6863 (tttm) REVERT: F 132 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7815 (mm-40) REVERT: F 145 ARG cc_start: 0.8378 (mmp80) cc_final: 0.7823 (mmm160) REVERT: G 164 GLN cc_start: 0.8191 (tp40) cc_final: 0.7625 (tp40) REVERT: G 174 TRP cc_start: 0.7910 (m100) cc_final: 0.7316 (m100) REVERT: G 183 TYR cc_start: 0.7242 (t80) cc_final: 0.6981 (t80) REVERT: H 75 MET cc_start: 0.8459 (mmt) cc_final: 0.8055 (tpp) REVERT: H 78 TYR cc_start: 0.8594 (t80) cc_final: 0.8069 (t80) REVERT: H 119 GLU cc_start: 0.8105 (tp30) cc_final: 0.7865 (tp30) REVERT: H 121 MET cc_start: 0.7787 (tmm) cc_final: 0.7494 (tmm) REVERT: H 126 LEU cc_start: 0.7628 (pt) cc_final: 0.7338 (pt) REVERT: H 138 ILE cc_start: 0.8868 (mt) cc_final: 0.8583 (mm) REVERT: I 42 ASN cc_start: 0.8971 (t0) cc_final: 0.8260 (t0) REVERT: I 59 ASP cc_start: 0.6407 (p0) cc_final: 0.6050 (p0) REVERT: I 65 ASN cc_start: 0.8397 (t0) cc_final: 0.7820 (t0) REVERT: I 119 GLU cc_start: 0.5636 (mm-30) cc_final: 0.5051 (mm-30) REVERT: I 151 ASN cc_start: 0.8643 (m-40) cc_final: 0.8349 (m110) REVERT: I 160 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7436 (mp10) REVERT: I 167 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7976 (ttp-110) REVERT: I 170 ASP cc_start: 0.7468 (m-30) cc_final: 0.7244 (m-30) REVERT: J 1 MET cc_start: 0.3310 (ttt) cc_final: 0.2875 (ttm) REVERT: J 23 ARG cc_start: 0.7996 (tmt-80) cc_final: 0.7550 (tmt-80) REVERT: J 42 ASN cc_start: 0.8371 (m110) cc_final: 0.7555 (m-40) REVERT: J 57 GLU cc_start: 0.7732 (pm20) cc_final: 0.7424 (mp0) REVERT: J 58 LYS cc_start: 0.5925 (tttt) cc_final: 0.5723 (mptt) REVERT: J 81 MET cc_start: 0.7591 (mtm) cc_final: 0.7358 (mtt) REVERT: J 137 GLU cc_start: 0.8152 (pp20) cc_final: 0.7885 (pp20) REVERT: J 142 HIS cc_start: 0.8791 (t70) cc_final: 0.8220 (t70) REVERT: J 151 ASN cc_start: 0.7987 (m110) cc_final: 0.7757 (m110) REVERT: K 18 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5578 (p90) REVERT: K 26 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: K 31 MET cc_start: 0.8104 (tpt) cc_final: 0.7013 (ttp) REVERT: K 42 ASN cc_start: 0.8664 (t0) cc_final: 0.8036 (t0) REVERT: K 63 TYR cc_start: 0.7449 (m-80) cc_final: 0.7211 (m-80) REVERT: K 79 ASP cc_start: 0.8537 (m-30) cc_final: 0.8060 (m-30) REVERT: K 95 MET cc_start: 0.8152 (ttp) cc_final: 0.7866 (ttm) REVERT: K 137 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8039 (tm-30) REVERT: K 144 LEU cc_start: 0.8953 (tt) cc_final: 0.8708 (tp) REVERT: L 1 MET cc_start: 0.5201 (mtm) cc_final: 0.4914 (mtm) REVERT: L 4 ILE cc_start: 0.7606 (pt) cc_final: 0.7227 (mm) REVERT: L 23 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7337 (tpt90) REVERT: L 32 LEU cc_start: 0.8992 (tp) cc_final: 0.8564 (tt) REVERT: L 65 ASN cc_start: 0.8810 (t0) cc_final: 0.8480 (t0) REVERT: L 83 PHE cc_start: 0.8110 (t80) cc_final: 0.7846 (t80) REVERT: L 90 THR cc_start: 0.8992 (m) cc_final: 0.8713 (p) REVERT: L 95 MET cc_start: 0.7920 (tpt) cc_final: 0.7464 (tpt) REVERT: L 115 LEU cc_start: 0.9126 (mt) cc_final: 0.8700 (mt) REVERT: L 117 ASN cc_start: 0.8838 (m-40) cc_final: 0.8595 (m110) REVERT: L 132 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7243 (mm-40) REVERT: L 135 GLU cc_start: 0.8394 (mp0) cc_final: 0.7900 (mp0) REVERT: L 172 ASP cc_start: 0.8187 (p0) cc_final: 0.7829 (p0) REVERT: M 119 GLU cc_start: 0.7620 (mp0) cc_final: 0.7236 (mp0) REVERT: M 147 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8437 (tptt) REVERT: M 162 TYR cc_start: 0.8056 (t80) cc_final: 0.7697 (t80) REVERT: M 163 GLU cc_start: 0.8645 (mp0) cc_final: 0.8210 (pm20) REVERT: M 167 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.7844 (ttp-110) REVERT: M 170 ASP cc_start: 0.8586 (t70) cc_final: 0.7616 (m-30) REVERT: M 171 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7441 (mmt180) REVERT: M 190 ILE cc_start: 0.8224 (pt) cc_final: 0.7732 (tt) REVERT: N 1 MET cc_start: 0.3339 (mpp) cc_final: 0.1852 (tmm) REVERT: N 28 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7661 (mtp85) REVERT: N 36 ILE cc_start: 0.8429 (mt) cc_final: 0.8081 (mm) REVERT: N 55 ASP cc_start: 0.7055 (t0) cc_final: 0.6742 (t0) REVERT: N 121 MET cc_start: 0.6834 (tmm) cc_final: 0.6578 (tmm) REVERT: N 123 HIS cc_start: 0.8023 (t-170) cc_final: 0.7633 (t70) REVERT: N 132 GLN cc_start: 0.8154 (mt0) cc_final: 0.7803 (mt0) REVERT: N 137 GLU cc_start: 0.8258 (tp30) cc_final: 0.8021 (tm-30) REVERT: N 145 LYS cc_start: 0.8682 (mttt) cc_final: 0.8445 (mptt) REVERT: N 147 LYS cc_start: 0.8725 (pttp) cc_final: 0.8372 (pttp) REVERT: N 157 LYS cc_start: 0.8665 (mptt) cc_final: 0.8316 (mmmm) REVERT: N 172 ASP cc_start: 0.7843 (p0) cc_final: 0.7639 (p0) outliers start: 78 outliers final: 43 residues processed: 854 average time/residue: 0.1510 time to fit residues: 192.9106 Evaluate side-chains 759 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 712 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 170 ASP Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 249 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS A 151 ASN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN H 65 ASN H 117 ASN H 160 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN J 89 GLN L 89 GLN L 124 GLN L 151 ASN M 42 ASN M 65 ASN N 65 ASN N 132 GLN N 178 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096215 restraints weight = 49759.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099054 restraints weight = 27474.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101085 restraints weight = 17309.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102502 restraints weight = 11899.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103518 restraints weight = 8773.848| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20457 Z= 0.179 Angle : 0.716 10.164 27624 Z= 0.371 Chirality : 0.047 0.260 3206 Planarity : 0.005 0.089 3597 Dihedral : 6.026 88.213 2784 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 4.80 % Allowed : 22.75 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 2562 helix: -0.20 (0.13), residues: 1372 sheet: -1.11 (0.33), residues: 218 loop : -1.90 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 23 TYR 0.031 0.002 TYR E 104 PHE 0.021 0.002 PHE M 61 TRP 0.039 0.004 TRP A 95 HIS 0.012 0.002 HIS L 123 Details of bonding type rmsd covalent geometry : bond 0.00406 (20456) covalent geometry : angle 0.71634 (27624) hydrogen bonds : bond 0.03672 ( 977) hydrogen bonds : angle 5.00055 ( 2865) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 818 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8365 (t70) cc_final: 0.7885 (t-170) REVERT: A 75 ASP cc_start: 0.7552 (m-30) cc_final: 0.6492 (t0) REVERT: A 78 HIS cc_start: 0.8508 (t-90) cc_final: 0.7936 (t70) REVERT: A 79 ASP cc_start: 0.7754 (m-30) cc_final: 0.6404 (m-30) REVERT: A 132 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8443 (mm-40) REVERT: A 137 GLU cc_start: 0.8672 (tp30) cc_final: 0.8429 (tp30) REVERT: A 153 LEU cc_start: 0.9355 (mp) cc_final: 0.9142 (mp) REVERT: B 78 HIS cc_start: 0.7945 (t70) cc_final: 0.7542 (t70) REVERT: B 113 PHE cc_start: 0.7885 (m-80) cc_final: 0.7200 (m-80) REVERT: B 121 MET cc_start: 0.8366 (tmm) cc_final: 0.7037 (mmm) REVERT: B 135 GLU cc_start: 0.8110 (tt0) cc_final: 0.7873 (tm-30) REVERT: B 139 GLU cc_start: 0.8048 (tt0) cc_final: 0.7812 (tp30) REVERT: C 89 LYS cc_start: 0.6122 (mttt) cc_final: 0.5895 (mttm) REVERT: C 133 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.9034 (t) REVERT: C 165 ILE cc_start: 0.9134 (mt) cc_final: 0.8849 (mm) REVERT: C 172 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8066 (t0) REVERT: D 43 GLU cc_start: 0.8561 (tp30) cc_final: 0.8136 (tp30) REVERT: D 47 LYS cc_start: 0.8183 (tttt) cc_final: 0.7493 (ttmm) REVERT: D 79 ASP cc_start: 0.8503 (m-30) cc_final: 0.8259 (m-30) REVERT: D 124 GLN cc_start: 0.8548 (pm20) cc_final: 0.8253 (pm20) REVERT: D 147 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8238 (tmm-80) REVERT: D 174 TRP cc_start: 0.8331 (m100) cc_final: 0.7607 (m100) REVERT: E 43 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6866 (tm-30) REVERT: E 47 LYS cc_start: 0.7318 (tttt) cc_final: 0.6304 (tttt) REVERT: E 124 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: E 153 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8412 (mt) REVERT: E 170 ASP cc_start: 0.8100 (p0) cc_final: 0.7834 (p0) REVERT: F 47 LYS cc_start: 0.7598 (tttt) cc_final: 0.7036 (tttm) REVERT: F 119 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: F 142 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7588 (mm-30) REVERT: F 145 ARG cc_start: 0.8472 (mmp80) cc_final: 0.8120 (mmp80) REVERT: G 164 GLN cc_start: 0.8348 (tp40) cc_final: 0.8036 (tp-100) REVERT: G 183 TYR cc_start: 0.7019 (t80) cc_final: 0.6409 (t80) REVERT: H 38 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6976 (t0) REVERT: H 39 ASN cc_start: 0.8302 (m-40) cc_final: 0.7952 (m-40) REVERT: H 75 MET cc_start: 0.8485 (mmt) cc_final: 0.8204 (tpp) REVERT: H 78 TYR cc_start: 0.8641 (t80) cc_final: 0.8065 (t80) REVERT: H 87 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7254 (t70) REVERT: H 89 GLN cc_start: 0.7966 (pt0) cc_final: 0.7575 (pm20) REVERT: H 121 MET cc_start: 0.7840 (tmm) cc_final: 0.7193 (tmm) REVERT: H 126 LEU cc_start: 0.7564 (pt) cc_final: 0.7228 (pt) REVERT: I 18 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5705 (p90) REVERT: I 65 ASN cc_start: 0.8460 (t0) cc_final: 0.7409 (t0) REVERT: I 119 GLU cc_start: 0.5491 (mm-30) cc_final: 0.5093 (mm-30) REVERT: I 160 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7479 (mp10) REVERT: I 185 LEU cc_start: 0.8346 (mm) cc_final: 0.7798 (tp) REVERT: J 1 MET cc_start: 0.3725 (ttt) cc_final: 0.3416 (ttt) REVERT: J 23 ARG cc_start: 0.7875 (tmt-80) cc_final: 0.7233 (tmt-80) REVERT: J 42 ASN cc_start: 0.8321 (m110) cc_final: 0.7621 (m-40) REVERT: J 81 MET cc_start: 0.7551 (mtm) cc_final: 0.7322 (mtt) REVERT: J 132 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8224 (mm110) REVERT: J 137 GLU cc_start: 0.8314 (pp20) cc_final: 0.8104 (pp20) REVERT: J 151 ASN cc_start: 0.7911 (m110) cc_final: 0.7691 (m110) REVERT: K 18 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5657 (p90) REVERT: K 23 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8070 (ttm170) REVERT: K 26 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8195 (tttt) REVERT: K 31 MET cc_start: 0.8096 (tpt) cc_final: 0.7017 (ttp) REVERT: K 37 ASP cc_start: 0.7429 (t70) cc_final: 0.6724 (p0) REVERT: K 42 ASN cc_start: 0.8654 (t0) cc_final: 0.7925 (t0) REVERT: K 65 ASN cc_start: 0.7583 (t0) cc_final: 0.7213 (t0) REVERT: K 79 ASP cc_start: 0.8519 (m-30) cc_final: 0.7966 (m-30) REVERT: K 95 MET cc_start: 0.8181 (ttp) cc_final: 0.7868 (ttm) REVERT: K 112 ARG cc_start: 0.7300 (mtt90) cc_final: 0.7099 (mtt90) REVERT: K 147 LYS cc_start: 0.9011 (ptmt) cc_final: 0.8647 (ttpt) REVERT: L 1 MET cc_start: 0.4465 (mtm) cc_final: 0.4200 (mtm) REVERT: L 4 ILE cc_start: 0.7607 (pt) cc_final: 0.7257 (mm) REVERT: L 23 ARG cc_start: 0.7851 (tpt90) cc_final: 0.7649 (tpt90) REVERT: L 24 LEU cc_start: 0.9303 (mm) cc_final: 0.9100 (mm) REVERT: L 32 LEU cc_start: 0.8974 (tp) cc_final: 0.8588 (tt) REVERT: L 61 PHE cc_start: 0.7635 (m-80) cc_final: 0.7339 (m-10) REVERT: L 63 TYR cc_start: 0.7257 (m-80) cc_final: 0.6740 (m-80) REVERT: L 65 ASN cc_start: 0.8816 (t0) cc_final: 0.8580 (t0) REVERT: L 115 LEU cc_start: 0.9102 (mt) cc_final: 0.8668 (mt) REVERT: L 117 ASN cc_start: 0.8856 (m-40) cc_final: 0.8438 (m110) REVERT: L 135 GLU cc_start: 0.8391 (mp0) cc_final: 0.8059 (mp0) REVERT: L 172 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7865 (p0) REVERT: M 23 ARG cc_start: 0.7780 (tpt90) cc_final: 0.7374 (tpm170) REVERT: M 27 ASP cc_start: 0.7726 (m-30) cc_final: 0.7458 (m-30) REVERT: M 32 LEU cc_start: 0.9084 (tt) cc_final: 0.8539 (tt) REVERT: M 79 ASP cc_start: 0.8646 (m-30) cc_final: 0.7911 (m-30) REVERT: M 93 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7098 (ptt) REVERT: M 119 GLU cc_start: 0.7598 (mp0) cc_final: 0.7274 (mp0) REVERT: M 163 GLU cc_start: 0.8575 (mp0) cc_final: 0.8251 (pm20) REVERT: M 167 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: M 168 ASP cc_start: 0.7452 (m-30) cc_final: 0.7215 (m-30) REVERT: M 170 ASP cc_start: 0.8691 (t70) cc_final: 0.7572 (m-30) REVERT: M 171 ARG cc_start: 0.8029 (mmt180) cc_final: 0.7701 (mmt180) REVERT: M 190 ILE cc_start: 0.8277 (pt) cc_final: 0.7800 (tt) REVERT: N 1 MET cc_start: 0.3341 (mpp) cc_final: 0.1908 (tmm) REVERT: N 28 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7863 (mtp85) REVERT: N 36 ILE cc_start: 0.8478 (mt) cc_final: 0.8212 (mm) REVERT: N 55 ASP cc_start: 0.7359 (t0) cc_final: 0.6940 (t0) REVERT: N 61 PHE cc_start: 0.7546 (m-80) cc_final: 0.7133 (m-10) REVERT: N 111 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7928 (ttmt) REVERT: N 123 HIS cc_start: 0.8309 (t-170) cc_final: 0.7537 (t-170) REVERT: N 132 GLN cc_start: 0.8108 (mt0) cc_final: 0.7881 (mt0) REVERT: N 137 GLU cc_start: 0.8240 (tp30) cc_final: 0.7522 (tm-30) REVERT: N 141 ARG cc_start: 0.8044 (ptp-110) cc_final: 0.7689 (ptp-110) REVERT: N 144 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8649 (mm) REVERT: N 145 LYS cc_start: 0.8729 (mttt) cc_final: 0.8303 (mmtm) REVERT: N 147 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (pttp) REVERT: N 150 MET cc_start: 0.8705 (tpp) cc_final: 0.8256 (tpp) REVERT: N 157 LYS cc_start: 0.8600 (mptt) cc_final: 0.8286 (mmmm) REVERT: N 172 ASP cc_start: 0.7797 (p0) cc_final: 0.7375 (p0) outliers start: 104 outliers final: 57 residues processed: 867 average time/residue: 0.1543 time to fit residues: 199.7141 Evaluate side-chains 799 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 729 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 147 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN F 160 GLN F 164 GLN G 48 GLN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN I 42 ASN I 47 GLN I 151 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 65 ASN M 89 GLN ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095990 restraints weight = 49931.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098790 restraints weight = 27565.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100755 restraints weight = 17431.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102123 restraints weight = 12076.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102986 restraints weight = 9020.274| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20457 Z= 0.184 Angle : 0.727 11.816 27624 Z= 0.376 Chirality : 0.047 0.235 3206 Planarity : 0.005 0.064 3597 Dihedral : 5.909 87.028 2784 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 4.89 % Allowed : 25.01 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2562 helix: -0.01 (0.13), residues: 1358 sheet: -0.98 (0.33), residues: 236 loop : -1.77 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 145 TYR 0.030 0.002 TYR E 104 PHE 0.030 0.002 PHE M 83 TRP 0.025 0.004 TRP C 95 HIS 0.008 0.002 HIS H 142 Details of bonding type rmsd covalent geometry : bond 0.00419 (20456) covalent geometry : angle 0.72746 (27624) hydrogen bonds : bond 0.03592 ( 977) hydrogen bonds : angle 4.95811 ( 2865) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 775 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.7652 (mt0) cc_final: 0.7202 (mm-40) REVERT: A 70 HIS cc_start: 0.8249 (t70) cc_final: 0.8041 (t70) REVERT: A 75 ASP cc_start: 0.7427 (m-30) cc_final: 0.6576 (t0) REVERT: A 78 HIS cc_start: 0.8512 (t-90) cc_final: 0.7932 (t70) REVERT: A 79 ASP cc_start: 0.7645 (m-30) cc_final: 0.6306 (m-30) REVERT: A 132 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8447 (mm-40) REVERT: A 153 LEU cc_start: 0.9354 (mp) cc_final: 0.9100 (mp) REVERT: B 78 HIS cc_start: 0.7857 (t70) cc_final: 0.7525 (t70) REVERT: B 121 MET cc_start: 0.8344 (tmm) cc_final: 0.7366 (mmm) REVERT: B 132 GLN cc_start: 0.8066 (mt0) cc_final: 0.7561 (mm-40) REVERT: C 89 LYS cc_start: 0.6254 (mttt) cc_final: 0.5970 (mttm) REVERT: C 95 TRP cc_start: 0.7150 (p90) cc_final: 0.6567 (p90) REVERT: C 165 ILE cc_start: 0.9126 (mt) cc_final: 0.8815 (mm) REVERT: C 167 LYS cc_start: 0.8493 (ptpp) cc_final: 0.8246 (mppt) REVERT: C 172 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8056 (t0) REVERT: D 43 GLU cc_start: 0.8638 (tp30) cc_final: 0.8174 (tp30) REVERT: D 47 LYS cc_start: 0.8165 (tttt) cc_final: 0.7474 (ttmm) REVERT: D 79 ASP cc_start: 0.8560 (m-30) cc_final: 0.8291 (m-30) REVERT: D 124 GLN cc_start: 0.8632 (pm20) cc_final: 0.8274 (pm20) REVERT: D 170 ASP cc_start: 0.8172 (p0) cc_final: 0.7945 (m-30) REVERT: E 43 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6865 (tm-30) REVERT: E 47 LYS cc_start: 0.7125 (tttt) cc_final: 0.6274 (tttt) REVERT: E 124 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: E 146 MET cc_start: 0.8083 (ttm) cc_final: 0.7719 (ttm) REVERT: E 153 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8473 (mt) REVERT: E 170 ASP cc_start: 0.8146 (p0) cc_final: 0.7842 (p0) REVERT: F 47 LYS cc_start: 0.7519 (tttt) cc_final: 0.6976 (tttm) REVERT: F 119 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: F 142 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7599 (mm-30) REVERT: F 145 ARG cc_start: 0.8548 (mmp80) cc_final: 0.7992 (mmp80) REVERT: G 23 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6998 (tm-30) REVERT: G 43 GLU cc_start: 0.8285 (tt0) cc_final: 0.8024 (tt0) REVERT: G 72 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: G 95 TRP cc_start: 0.9075 (p-90) cc_final: 0.8340 (p-90) REVERT: G 164 GLN cc_start: 0.8443 (tp40) cc_final: 0.7497 (tp-100) REVERT: G 183 TYR cc_start: 0.7050 (t80) cc_final: 0.6510 (t80) REVERT: H 39 ASN cc_start: 0.8237 (m-40) cc_final: 0.7764 (m-40) REVERT: H 75 MET cc_start: 0.8566 (mmt) cc_final: 0.8213 (tpp) REVERT: H 78 TYR cc_start: 0.8725 (t80) cc_final: 0.8159 (t80) REVERT: H 85 LYS cc_start: 0.7787 (tptt) cc_final: 0.7508 (tptt) REVERT: H 87 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7149 (t70) REVERT: H 121 MET cc_start: 0.8009 (tmm) cc_final: 0.7371 (tmm) REVERT: H 122 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7688 (tt) REVERT: H 126 LEU cc_start: 0.7466 (pt) cc_final: 0.7266 (pt) REVERT: I 18 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5750 (p90) REVERT: I 23 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7661 (tpp-160) REVERT: I 42 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8107 (t0) REVERT: I 47 GLN cc_start: 0.8607 (mt0) cc_final: 0.8403 (mt0) REVERT: I 65 ASN cc_start: 0.8461 (t0) cc_final: 0.7777 (t0) REVERT: I 119 GLU cc_start: 0.5624 (mm-30) cc_final: 0.5255 (mm-30) REVERT: I 160 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7589 (mp10) REVERT: I 167 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7754 (ttp-110) REVERT: I 170 ASP cc_start: 0.7608 (m-30) cc_final: 0.7394 (m-30) REVERT: I 185 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7932 (tp) REVERT: J 1 MET cc_start: 0.3724 (ttt) cc_final: 0.3357 (ttt) REVERT: J 23 ARG cc_start: 0.7880 (tmt-80) cc_final: 0.7307 (tmt-80) REVERT: J 47 GLN cc_start: 0.8823 (pt0) cc_final: 0.8529 (pt0) REVERT: J 70 SER cc_start: 0.8955 (t) cc_final: 0.8458 (m) REVERT: J 132 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8131 (mm110) REVERT: J 151 ASN cc_start: 0.8000 (m110) cc_final: 0.7700 (m110) REVERT: K 18 TYR cc_start: 0.6028 (OUTLIER) cc_final: 0.5465 (p90) REVERT: K 23 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8028 (ttm170) REVERT: K 26 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8174 (tttt) REVERT: K 37 ASP cc_start: 0.7500 (t70) cc_final: 0.6846 (p0) REVERT: K 42 ASN cc_start: 0.8654 (t0) cc_final: 0.7938 (t0) REVERT: K 49 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8016 (mm) REVERT: K 65 ASN cc_start: 0.7662 (t0) cc_final: 0.7367 (t0) REVERT: K 79 ASP cc_start: 0.8560 (m-30) cc_final: 0.8075 (m-30) REVERT: K 95 MET cc_start: 0.8274 (ttp) cc_final: 0.7667 (ttm) REVERT: L 1 MET cc_start: 0.4453 (mtm) cc_final: 0.4246 (mtm) REVERT: L 4 ILE cc_start: 0.7446 (pt) cc_final: 0.7166 (mm) REVERT: L 32 LEU cc_start: 0.8992 (tp) cc_final: 0.8547 (tt) REVERT: L 63 TYR cc_start: 0.7327 (m-80) cc_final: 0.6829 (m-80) REVERT: L 65 ASN cc_start: 0.8766 (t0) cc_final: 0.8518 (t0) REVERT: L 75 MET cc_start: 0.8021 (mmp) cc_final: 0.7737 (mmm) REVERT: L 85 LYS cc_start: 0.7951 (tttt) cc_final: 0.7613 (ttmt) REVERT: L 115 LEU cc_start: 0.9070 (mt) cc_final: 0.8668 (mt) REVERT: L 117 ASN cc_start: 0.8819 (m-40) cc_final: 0.8439 (m110) REVERT: L 149 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7477 (mmm-85) REVERT: L 150 MET cc_start: 0.8070 (mmp) cc_final: 0.7711 (mmp) REVERT: L 172 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7851 (p0) REVERT: M 23 ARG cc_start: 0.7874 (tpt90) cc_final: 0.7602 (tpm170) REVERT: M 63 TYR cc_start: 0.6652 (m-10) cc_final: 0.6394 (m-80) REVERT: M 79 ASP cc_start: 0.8663 (m-30) cc_final: 0.7968 (m-30) REVERT: M 93 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7110 (ptt) REVERT: M 119 GLU cc_start: 0.7736 (mp0) cc_final: 0.7272 (mp0) REVERT: M 163 GLU cc_start: 0.8551 (mp0) cc_final: 0.8221 (pm20) REVERT: M 167 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7909 (ttp-110) REVERT: M 170 ASP cc_start: 0.8535 (t70) cc_final: 0.7774 (m-30) REVERT: M 190 ILE cc_start: 0.8280 (pt) cc_final: 0.7745 (tt) REVERT: N 1 MET cc_start: 0.3140 (mpp) cc_final: 0.1710 (tmm) REVERT: N 23 ARG cc_start: 0.9071 (tpp-160) cc_final: 0.8865 (tpp-160) REVERT: N 28 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8091 (mtp85) REVERT: N 36 ILE cc_start: 0.8655 (mt) cc_final: 0.8405 (mm) REVERT: N 47 GLN cc_start: 0.8346 (mt0) cc_final: 0.7899 (mm-40) REVERT: N 55 ASP cc_start: 0.7162 (t0) cc_final: 0.6951 (t0) REVERT: N 65 ASN cc_start: 0.8207 (t0) cc_final: 0.7723 (t0) REVERT: N 87 ASP cc_start: 0.6209 (m-30) cc_final: 0.6008 (m-30) REVERT: N 123 HIS cc_start: 0.8239 (t-170) cc_final: 0.7393 (t70) REVERT: N 132 GLN cc_start: 0.8115 (mt0) cc_final: 0.7895 (mt0) REVERT: N 145 LYS cc_start: 0.8752 (mttt) cc_final: 0.8358 (mmtt) REVERT: N 147 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8450 (pttp) REVERT: N 157 LYS cc_start: 0.8574 (mptt) cc_final: 0.8330 (mmmm) REVERT: N 172 ASP cc_start: 0.7679 (p0) cc_final: 0.7339 (p0) REVERT: N 181 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8457 (ttmt) outliers start: 106 outliers final: 63 residues processed: 823 average time/residue: 0.1506 time to fit residues: 186.2778 Evaluate side-chains 798 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 720 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN B 70 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN F 164 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN I 151 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 160 GLN K 47 GLN ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 65 ASN M 89 GLN ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 142 HIS N 178 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096798 restraints weight = 49570.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099577 restraints weight = 27452.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101552 restraints weight = 17316.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102915 restraints weight = 11987.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103901 restraints weight = 8931.688| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20457 Z= 0.163 Angle : 0.736 10.592 27624 Z= 0.375 Chirality : 0.047 0.259 3206 Planarity : 0.005 0.067 3597 Dihedral : 5.767 87.662 2784 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 4.98 % Allowed : 25.70 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2562 helix: -0.01 (0.13), residues: 1392 sheet: -1.09 (0.32), residues: 251 loop : -1.80 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 23 TYR 0.026 0.002 TYR E 104 PHE 0.037 0.002 PHE I 174 TRP 0.022 0.003 TRP A 95 HIS 0.008 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00377 (20456) covalent geometry : angle 0.73618 (27624) hydrogen bonds : bond 0.03426 ( 977) hydrogen bonds : angle 4.86978 ( 2865) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 771 time to evaluate : 0.633 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 47 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8041 (mmtp) REVERT: A 70 HIS cc_start: 0.8250 (t70) cc_final: 0.8004 (t70) REVERT: A 75 ASP cc_start: 0.7414 (m-30) cc_final: 0.6484 (t0) REVERT: A 78 HIS cc_start: 0.8541 (t-90) cc_final: 0.8027 (t70) REVERT: A 79 ASP cc_start: 0.7651 (m-30) cc_final: 0.6299 (m-30) REVERT: A 137 GLU cc_start: 0.8368 (tp30) cc_final: 0.8132 (tp30) REVERT: A 167 LYS cc_start: 0.8443 (pttp) cc_final: 0.7830 (pttp) REVERT: B 78 HIS cc_start: 0.7867 (t70) cc_final: 0.7548 (t70) REVERT: B 113 PHE cc_start: 0.7889 (m-80) cc_final: 0.7219 (m-80) REVERT: B 142 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6865 (mt-10) REVERT: B 145 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8365 (ttp-110) REVERT: C 89 LYS cc_start: 0.6174 (mttt) cc_final: 0.5928 (mttm) REVERT: C 119 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7124 (mtp180) REVERT: C 132 GLN cc_start: 0.8720 (mt0) cc_final: 0.8350 (mt0) REVERT: D 39 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7618 (mt0) REVERT: D 43 GLU cc_start: 0.8619 (tp30) cc_final: 0.8408 (tp30) REVERT: D 47 LYS cc_start: 0.8145 (tttt) cc_final: 0.7521 (ttmm) REVERT: D 79 ASP cc_start: 0.8569 (m-30) cc_final: 0.8277 (m-30) REVERT: D 121 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7065 (ttm) REVERT: D 124 GLN cc_start: 0.8682 (pm20) cc_final: 0.8208 (pm20) REVERT: E 43 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6844 (tm-30) REVERT: E 47 LYS cc_start: 0.7079 (tttt) cc_final: 0.6296 (tttt) REVERT: E 124 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: E 129 VAL cc_start: 0.8905 (p) cc_final: 0.8546 (m) REVERT: E 153 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8465 (mt) REVERT: E 170 ASP cc_start: 0.8148 (p0) cc_final: 0.7886 (p0) REVERT: F 47 LYS cc_start: 0.7590 (tttt) cc_final: 0.7200 (mtpp) REVERT: F 70 HIS cc_start: 0.7777 (t-90) cc_final: 0.7476 (t70) REVERT: F 119 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: F 137 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7742 (tm-30) REVERT: F 142 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 145 ARG cc_start: 0.8523 (mmp80) cc_final: 0.8032 (mmp80) REVERT: G 23 GLN cc_start: 0.7332 (tm-30) cc_final: 0.6944 (tm-30) REVERT: G 121 MET cc_start: 0.6768 (ttm) cc_final: 0.6509 (ttm) REVERT: G 164 GLN cc_start: 0.8530 (tp40) cc_final: 0.7666 (tp-100) REVERT: G 183 TYR cc_start: 0.7046 (t80) cc_final: 0.6799 (t80) REVERT: H 1 MET cc_start: 0.3459 (tpp) cc_final: 0.3170 (tpt) REVERT: H 38 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.6859 (t0) REVERT: H 39 ASN cc_start: 0.8161 (m-40) cc_final: 0.7727 (m-40) REVERT: H 75 MET cc_start: 0.8419 (mmt) cc_final: 0.8140 (tpp) REVERT: H 78 TYR cc_start: 0.8755 (t80) cc_final: 0.8274 (t80) REVERT: H 85 LYS cc_start: 0.7754 (tptt) cc_final: 0.7457 (tptt) REVERT: H 87 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7245 (t70) REVERT: H 121 MET cc_start: 0.8033 (tmm) cc_final: 0.7443 (tmm) REVERT: H 122 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7866 (tt) REVERT: H 148 GLU cc_start: 0.8534 (tt0) cc_final: 0.8286 (tm-30) REVERT: I 18 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5614 (p90) REVERT: I 23 ARG cc_start: 0.8179 (tpp-160) cc_final: 0.7642 (tpp-160) REVERT: I 65 ASN cc_start: 0.8383 (t0) cc_final: 0.7229 (t0) REVERT: I 75 MET cc_start: 0.8030 (tpp) cc_final: 0.7579 (tpp) REVERT: I 89 GLN cc_start: 0.8162 (mp10) cc_final: 0.7898 (mp10) REVERT: I 113 PHE cc_start: 0.7793 (m-80) cc_final: 0.7576 (m-80) REVERT: I 119 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5555 (mm-30) REVERT: I 151 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8023 (m110) REVERT: I 160 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7600 (mp10) REVERT: I 167 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8058 (ttp-110) REVERT: I 185 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7970 (tp) REVERT: J 1 MET cc_start: 0.3574 (ttt) cc_final: 0.3327 (ttt) REVERT: J 23 ARG cc_start: 0.7997 (tmt-80) cc_final: 0.7438 (tmt-80) REVERT: J 70 SER cc_start: 0.8941 (t) cc_final: 0.8416 (m) REVERT: J 71 ILE cc_start: 0.9059 (tp) cc_final: 0.8710 (pt) REVERT: J 151 ASN cc_start: 0.8013 (m110) cc_final: 0.7748 (m110) REVERT: K 18 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5520 (p90) REVERT: K 23 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7909 (ttm170) REVERT: K 26 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8124 (tttt) REVERT: K 37 ASP cc_start: 0.7467 (t70) cc_final: 0.6878 (p0) REVERT: K 42 ASN cc_start: 0.8507 (t0) cc_final: 0.7959 (t0) REVERT: K 49 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8049 (mm) REVERT: K 65 ASN cc_start: 0.7546 (t0) cc_final: 0.7166 (t0) REVERT: K 79 ASP cc_start: 0.8499 (m-30) cc_final: 0.8032 (m-30) REVERT: K 95 MET cc_start: 0.8300 (ttp) cc_final: 0.7835 (ttm) REVERT: K 147 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8706 (ttpt) REVERT: K 181 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7714 (tttp) REVERT: K 190 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6659 (pt) REVERT: L 1 MET cc_start: 0.4397 (mtm) cc_final: 0.4130 (mtm) REVERT: L 32 LEU cc_start: 0.8977 (tp) cc_final: 0.8542 (tt) REVERT: L 65 ASN cc_start: 0.8768 (t0) cc_final: 0.8539 (t0) REVERT: L 85 LYS cc_start: 0.7987 (tttt) cc_final: 0.7602 (ttmt) REVERT: L 93 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7168 (ptt) REVERT: L 117 ASN cc_start: 0.8811 (m-40) cc_final: 0.8369 (m110) REVERT: L 135 GLU cc_start: 0.8427 (mp0) cc_final: 0.7745 (mp0) REVERT: L 148 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8490 (mt-10) REVERT: L 149 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.7528 (mmm-85) REVERT: L 150 MET cc_start: 0.8059 (mmp) cc_final: 0.7798 (mmp) REVERT: L 172 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7773 (p0) REVERT: M 23 ARG cc_start: 0.7962 (tpt90) cc_final: 0.7528 (tpm170) REVERT: M 27 ASP cc_start: 0.7262 (t70) cc_final: 0.7058 (t70) REVERT: M 38 ASP cc_start: 0.7129 (m-30) cc_final: 0.6520 (t0) REVERT: M 79 ASP cc_start: 0.8624 (m-30) cc_final: 0.7894 (m-30) REVERT: M 89 GLN cc_start: 0.7283 (pt0) cc_final: 0.7033 (pt0) REVERT: M 149 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8001 (ttp80) REVERT: M 163 GLU cc_start: 0.8507 (mp0) cc_final: 0.8220 (pm20) REVERT: M 167 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.7972 (ttp-110) REVERT: M 170 ASP cc_start: 0.8520 (t70) cc_final: 0.7573 (m-30) REVERT: M 171 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7912 (mmt90) REVERT: M 190 ILE cc_start: 0.8077 (pt) cc_final: 0.7597 (tt) REVERT: N 1 MET cc_start: 0.3163 (mpp) cc_final: 0.1736 (tmm) REVERT: N 26 LYS cc_start: 0.7538 (tttp) cc_final: 0.7225 (pttt) REVERT: N 31 MET cc_start: 0.8256 (mmm) cc_final: 0.7720 (ttm) REVERT: N 36 ILE cc_start: 0.8718 (mt) cc_final: 0.8434 (mm) REVERT: N 55 ASP cc_start: 0.7148 (t0) cc_final: 0.6816 (t0) REVERT: N 89 GLN cc_start: 0.7839 (mt0) cc_final: 0.7446 (tt0) REVERT: N 123 HIS cc_start: 0.8182 (t-170) cc_final: 0.7393 (t-170) REVERT: N 132 GLN cc_start: 0.8149 (mt0) cc_final: 0.7838 (mt0) REVERT: N 137 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7067 (tp30) REVERT: N 145 LYS cc_start: 0.8738 (mttt) cc_final: 0.8448 (mmtt) REVERT: N 147 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8457 (pttp) REVERT: N 157 LYS cc_start: 0.8614 (mptt) cc_final: 0.8220 (mmmm) REVERT: N 167 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8131 (ptp90) REVERT: N 172 ASP cc_start: 0.7626 (p0) cc_final: 0.7231 (p0) REVERT: N 181 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8505 (ttmm) outliers start: 108 outliers final: 68 residues processed: 823 average time/residue: 0.1471 time to fit residues: 183.3615 Evaluate side-chains 807 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 722 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 131 optimal weight: 0.0870 chunk 248 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 overall best weight: 2.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN I 151 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN N 178 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096070 restraints weight = 50221.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098798 restraints weight = 28028.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100786 restraints weight = 17769.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102153 restraints weight = 12273.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103154 restraints weight = 9120.919| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20457 Z= 0.177 Angle : 0.750 12.199 27624 Z= 0.384 Chirality : 0.048 0.268 3206 Planarity : 0.004 0.061 3597 Dihedral : 5.733 87.299 2784 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 4.75 % Allowed : 27.04 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2562 helix: 0.04 (0.13), residues: 1393 sheet: -1.09 (0.33), residues: 251 loop : -1.80 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 112 TYR 0.028 0.002 TYR E 104 PHE 0.033 0.002 PHE D 173 TRP 0.028 0.003 TRP G 174 HIS 0.010 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00409 (20456) covalent geometry : angle 0.74977 (27624) hydrogen bonds : bond 0.03428 ( 977) hydrogen bonds : angle 4.84540 ( 2865) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 768 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 47 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8027 (mmtp) REVERT: A 70 HIS cc_start: 0.8299 (t70) cc_final: 0.7790 (t-170) REVERT: A 75 ASP cc_start: 0.7478 (m-30) cc_final: 0.6611 (t0) REVERT: A 79 ASP cc_start: 0.7684 (m-30) cc_final: 0.6782 (m-30) REVERT: A 167 LYS cc_start: 0.8642 (pttp) cc_final: 0.8136 (pttp) REVERT: B 78 HIS cc_start: 0.7939 (t70) cc_final: 0.7568 (t70) REVERT: B 121 MET cc_start: 0.8354 (tmm) cc_final: 0.7337 (mmm) REVERT: B 139 GLU cc_start: 0.8106 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 89 LYS cc_start: 0.6120 (mttt) cc_final: 0.5883 (mttm) REVERT: C 95 TRP cc_start: 0.7200 (p90) cc_final: 0.6788 (p90) REVERT: C 119 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7078 (mtp180) REVERT: C 132 GLN cc_start: 0.8839 (mt0) cc_final: 0.8613 (mt0) REVERT: D 43 GLU cc_start: 0.8645 (tp30) cc_final: 0.8425 (tp30) REVERT: D 47 LYS cc_start: 0.8188 (tttt) cc_final: 0.7560 (ttmm) REVERT: D 79 ASP cc_start: 0.8578 (m-30) cc_final: 0.8302 (m-30) REVERT: D 124 GLN cc_start: 0.8704 (pm20) cc_final: 0.8222 (pm20) REVERT: D 167 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8782 (mtmt) REVERT: E 43 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6824 (tm-30) REVERT: E 47 LYS cc_start: 0.7062 (tttt) cc_final: 0.6281 (tttt) REVERT: E 124 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: E 170 ASP cc_start: 0.8157 (p0) cc_final: 0.7858 (p0) REVERT: F 24 LYS cc_start: 0.6584 (mmtm) cc_final: 0.6352 (mmtp) REVERT: F 47 LYS cc_start: 0.7478 (tttt) cc_final: 0.7216 (mtpp) REVERT: F 48 GLN cc_start: 0.8715 (mm110) cc_final: 0.8422 (mp10) REVERT: F 70 HIS cc_start: 0.7837 (t-90) cc_final: 0.7627 (t70) REVERT: F 137 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7935 (tm-30) REVERT: F 145 ARG cc_start: 0.8536 (mmp80) cc_final: 0.8008 (mmp80) REVERT: G 23 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7082 (tm-30) REVERT: G 95 TRP cc_start: 0.9060 (p-90) cc_final: 0.8620 (p-90) REVERT: G 146 MET cc_start: 0.7461 (mmp) cc_final: 0.7166 (mmp) REVERT: G 164 GLN cc_start: 0.8555 (tp40) cc_final: 0.7645 (tp-100) REVERT: H 1 MET cc_start: 0.3551 (tpp) cc_final: 0.3305 (tpt) REVERT: H 38 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6743 (t0) REVERT: H 39 ASN cc_start: 0.8089 (m-40) cc_final: 0.7717 (m-40) REVERT: H 75 MET cc_start: 0.8470 (mmt) cc_final: 0.8218 (tpp) REVERT: H 78 TYR cc_start: 0.8757 (t80) cc_final: 0.8247 (t80) REVERT: H 85 LYS cc_start: 0.7768 (tptt) cc_final: 0.7495 (tptt) REVERT: H 87 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7118 (t70) REVERT: H 183 TYR cc_start: 0.7466 (t80) cc_final: 0.7096 (t80) REVERT: I 1 MET cc_start: 0.4175 (mpp) cc_final: 0.2430 (ttt) REVERT: I 18 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5531 (p90) REVERT: I 23 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: I 42 ASN cc_start: 0.8823 (t160) cc_final: 0.8326 (t0) REVERT: I 65 ASN cc_start: 0.8337 (t0) cc_final: 0.7172 (t0) REVERT: I 89 GLN cc_start: 0.8095 (mp10) cc_final: 0.7830 (mp10) REVERT: I 113 PHE cc_start: 0.7777 (m-80) cc_final: 0.7505 (m-80) REVERT: I 119 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5560 (mm-30) REVERT: I 121 MET cc_start: 0.8073 (mmm) cc_final: 0.7516 (mmm) REVERT: I 124 GLN cc_start: 0.7765 (pm20) cc_final: 0.7271 (mp10) REVERT: I 151 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8041 (m110) REVERT: I 160 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7426 (mp10) REVERT: I 167 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8115 (ttp-110) REVERT: I 185 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8060 (tp) REVERT: J 1 MET cc_start: 0.3812 (ttt) cc_final: 0.3333 (ttt) REVERT: J 23 ARG cc_start: 0.7912 (tmt-80) cc_final: 0.7380 (tmt-80) REVERT: J 70 SER cc_start: 0.8914 (t) cc_final: 0.8351 (m) REVERT: J 71 ILE cc_start: 0.9090 (tp) cc_final: 0.8725 (pt) REVERT: J 151 ASN cc_start: 0.8002 (m110) cc_final: 0.7776 (m110) REVERT: K 18 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5468 (p90) REVERT: K 26 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: K 37 ASP cc_start: 0.7519 (t70) cc_final: 0.7265 (p0) REVERT: K 42 ASN cc_start: 0.8655 (t0) cc_final: 0.8010 (t0) REVERT: K 49 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8074 (mm) REVERT: K 65 ASN cc_start: 0.7609 (t0) cc_final: 0.7270 (t0) REVERT: K 79 ASP cc_start: 0.8508 (m-30) cc_final: 0.8136 (m-30) REVERT: K 95 MET cc_start: 0.8258 (ttp) cc_final: 0.7818 (ttm) REVERT: K 124 GLN cc_start: 0.8476 (pt0) cc_final: 0.8236 (pt0) REVERT: K 137 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8362 (tm-30) REVERT: K 148 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8151 (pp20) REVERT: K 190 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6634 (pt) REVERT: L 32 LEU cc_start: 0.8981 (tp) cc_final: 0.8640 (tt) REVERT: L 63 TYR cc_start: 0.7242 (m-80) cc_final: 0.6558 (m-80) REVERT: L 65 ASN cc_start: 0.8843 (t0) cc_final: 0.8583 (t0) REVERT: L 85 LYS cc_start: 0.8015 (tttt) cc_final: 0.7713 (ttmt) REVERT: L 117 ASN cc_start: 0.8806 (m-40) cc_final: 0.8324 (m110) REVERT: L 135 GLU cc_start: 0.8512 (mp0) cc_final: 0.8242 (mp0) REVERT: L 148 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8542 (mt-10) REVERT: L 149 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7587 (mmm-85) REVERT: L 150 MET cc_start: 0.8094 (mmp) cc_final: 0.7892 (mmp) REVERT: L 172 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7835 (p0) REVERT: M 10 GLN cc_start: 0.3808 (mp10) cc_final: 0.3532 (mp10) REVERT: M 23 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7244 (tpp80) REVERT: M 27 ASP cc_start: 0.7412 (t70) cc_final: 0.7045 (t70) REVERT: M 63 TYR cc_start: 0.6768 (m-10) cc_final: 0.6341 (m-80) REVERT: M 79 ASP cc_start: 0.8620 (m-30) cc_final: 0.7945 (m-30) REVERT: M 89 GLN cc_start: 0.7301 (pt0) cc_final: 0.7062 (pt0) REVERT: M 99 MET cc_start: 0.8354 (tpt) cc_final: 0.7930 (tpt) REVERT: M 149 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7975 (ttp80) REVERT: M 163 GLU cc_start: 0.8550 (mp0) cc_final: 0.8257 (pm20) REVERT: M 167 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8033 (ttp-110) REVERT: M 169 THR cc_start: 0.8585 (m) cc_final: 0.8253 (t) REVERT: M 170 ASP cc_start: 0.8510 (t70) cc_final: 0.7486 (m-30) REVERT: M 190 ILE cc_start: 0.8095 (pt) cc_final: 0.7588 (tt) REVERT: N 1 MET cc_start: 0.3203 (mpp) cc_final: 0.1832 (tmm) REVERT: N 55 ASP cc_start: 0.6965 (t0) cc_final: 0.6623 (t0) REVERT: N 61 PHE cc_start: 0.7207 (m-80) cc_final: 0.6845 (m-10) REVERT: N 99 MET cc_start: 0.7018 (tpt) cc_final: 0.6510 (tpp) REVERT: N 111 LYS cc_start: 0.8013 (ptmm) cc_final: 0.6951 (ptmm) REVERT: N 123 HIS cc_start: 0.8104 (t-170) cc_final: 0.7333 (t-170) REVERT: N 132 GLN cc_start: 0.8155 (mt0) cc_final: 0.7688 (mt0) REVERT: N 137 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7215 (tm-30) REVERT: N 145 LYS cc_start: 0.8717 (mttt) cc_final: 0.8468 (mmtt) REVERT: N 147 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8506 (pttp) REVERT: N 150 MET cc_start: 0.8961 (tpp) cc_final: 0.8755 (tpp) REVERT: N 157 LYS cc_start: 0.8631 (mptt) cc_final: 0.8365 (mttm) REVERT: N 167 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8194 (mtp-110) REVERT: N 172 ASP cc_start: 0.7650 (p0) cc_final: 0.7202 (p0) REVERT: N 178 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8282 (pp30) outliers start: 103 outliers final: 70 residues processed: 818 average time/residue: 0.1467 time to fit residues: 181.2571 Evaluate side-chains 804 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 721 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 180 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 151 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN H 89 GLN H 124 GLN J 47 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 65 ASN ** M 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN N 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097894 restraints weight = 49594.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100665 restraints weight = 27483.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102661 restraints weight = 17385.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104054 restraints weight = 11949.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104893 restraints weight = 8782.679| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20457 Z= 0.150 Angle : 0.772 10.780 27624 Z= 0.389 Chirality : 0.048 0.307 3206 Planarity : 0.004 0.048 3597 Dihedral : 5.640 87.693 2784 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 4.01 % Allowed : 28.80 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2562 helix: 0.10 (0.13), residues: 1394 sheet: -0.97 (0.33), residues: 252 loop : -1.72 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 141 TYR 0.026 0.002 TYR E 104 PHE 0.025 0.002 PHE K 50 TRP 0.030 0.003 TRP G 174 HIS 0.008 0.002 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00353 (20456) covalent geometry : angle 0.77185 (27624) hydrogen bonds : bond 0.03316 ( 977) hydrogen bonds : angle 4.77728 ( 2865) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 763 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8045 (mmtp) REVERT: A 70 HIS cc_start: 0.8234 (t70) cc_final: 0.7698 (t-170) REVERT: A 132 GLN cc_start: 0.8925 (mt0) cc_final: 0.7928 (tt0) REVERT: A 167 LYS cc_start: 0.8621 (pttp) cc_final: 0.8218 (pttp) REVERT: B 78 HIS cc_start: 0.7902 (t70) cc_final: 0.7547 (t70) REVERT: B 113 PHE cc_start: 0.7960 (m-80) cc_final: 0.7317 (m-80) REVERT: B 121 MET cc_start: 0.8255 (tmm) cc_final: 0.7322 (mmm) REVERT: B 139 GLU cc_start: 0.8063 (tt0) cc_final: 0.7844 (tm-30) REVERT: B 142 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6788 (tt0) REVERT: C 89 LYS cc_start: 0.6145 (mttt) cc_final: 0.5895 (mttm) REVERT: C 95 TRP cc_start: 0.7193 (p90) cc_final: 0.6851 (p90) REVERT: C 119 ARG cc_start: 0.7621 (mtm180) cc_final: 0.6884 (mtp180) REVERT: C 132 GLN cc_start: 0.8603 (mt0) cc_final: 0.8215 (mt0) REVERT: D 39 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7613 (mt0) REVERT: D 43 GLU cc_start: 0.8595 (tp30) cc_final: 0.8368 (tp30) REVERT: D 47 LYS cc_start: 0.8185 (tttt) cc_final: 0.7570 (ttmm) REVERT: D 79 ASP cc_start: 0.8506 (m-30) cc_final: 0.8215 (m-30) REVERT: D 121 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6548 (ttm) REVERT: D 124 GLN cc_start: 0.8669 (pm20) cc_final: 0.8220 (pm20) REVERT: D 170 ASP cc_start: 0.8194 (p0) cc_final: 0.7955 (m-30) REVERT: D 174 TRP cc_start: 0.8332 (m100) cc_final: 0.7417 (m100) REVERT: E 38 ASN cc_start: 0.9211 (p0) cc_final: 0.8970 (p0) REVERT: E 43 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6791 (tm-30) REVERT: E 47 LYS cc_start: 0.7040 (tttt) cc_final: 0.6242 (tttt) REVERT: E 113 PHE cc_start: 0.7743 (m-10) cc_final: 0.7424 (m-10) REVERT: F 48 GLN cc_start: 0.8666 (mm110) cc_final: 0.8074 (mp10) REVERT: F 70 HIS cc_start: 0.7819 (t-90) cc_final: 0.7535 (t70) REVERT: F 119 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7754 (ttp-110) REVERT: F 132 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7858 (mm-40) REVERT: F 136 ILE cc_start: 0.9339 (mm) cc_final: 0.9083 (mm) REVERT: F 137 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7766 (tm-30) REVERT: G 167 LYS cc_start: 0.8920 (ptpp) cc_final: 0.8660 (mtmm) REVERT: H 38 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7174 (t0) REVERT: H 39 ASN cc_start: 0.8212 (m-40) cc_final: 0.7802 (m-40) REVERT: H 78 TYR cc_start: 0.8734 (t80) cc_final: 0.8238 (t80) REVERT: H 85 LYS cc_start: 0.7726 (tptt) cc_final: 0.7489 (tptt) REVERT: H 87 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7373 (t70) REVERT: H 121 MET cc_start: 0.7687 (tmm) cc_final: 0.7486 (tmm) REVERT: H 183 TYR cc_start: 0.7374 (t80) cc_final: 0.6918 (t80) REVERT: I 1 MET cc_start: 0.4332 (mpp) cc_final: 0.2232 (ttt) REVERT: I 18 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5129 (p90) REVERT: I 42 ASN cc_start: 0.8869 (t160) cc_final: 0.8667 (t0) REVERT: I 65 ASN cc_start: 0.8325 (t0) cc_final: 0.7252 (t0) REVERT: I 89 GLN cc_start: 0.8077 (mp10) cc_final: 0.7815 (mp10) REVERT: I 113 PHE cc_start: 0.7783 (m-80) cc_final: 0.7557 (m-80) REVERT: I 119 GLU cc_start: 0.6014 (mm-30) cc_final: 0.5526 (mm-30) REVERT: I 160 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7458 (mp10) REVERT: I 185 LEU cc_start: 0.8557 (mm) cc_final: 0.7914 (tp) REVERT: J 1 MET cc_start: 0.3697 (ttt) cc_final: 0.3277 (ttt) REVERT: J 70 SER cc_start: 0.8899 (t) cc_final: 0.8298 (m) REVERT: J 119 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7114 (tm-30) REVERT: J 132 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8015 (mm-40) REVERT: J 151 ASN cc_start: 0.8008 (m110) cc_final: 0.7715 (m110) REVERT: J 157 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8673 (mttm) REVERT: J 167 ARG cc_start: 0.8789 (ptm-80) cc_final: 0.8225 (ptm-80) REVERT: K 18 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5526 (p90) REVERT: K 26 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8066 (tttt) REVERT: K 42 ASN cc_start: 0.8597 (t0) cc_final: 0.8039 (t0) REVERT: K 65 ASN cc_start: 0.7439 (t0) cc_final: 0.7152 (t0) REVERT: K 79 ASP cc_start: 0.8505 (m-30) cc_final: 0.8073 (m-30) REVERT: K 95 MET cc_start: 0.8265 (ttp) cc_final: 0.7857 (ttm) REVERT: K 137 GLU cc_start: 0.8762 (tm-30) cc_final: 0.7964 (tm-30) REVERT: K 148 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8220 (pp20) REVERT: K 167 ARG cc_start: 0.8437 (ttp80) cc_final: 0.7989 (ttp80) REVERT: K 190 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6119 (pt) REVERT: L 23 ARG cc_start: 0.7860 (tpt90) cc_final: 0.7524 (tpt90) REVERT: L 32 LEU cc_start: 0.8884 (tp) cc_final: 0.8588 (tt) REVERT: L 85 LYS cc_start: 0.8007 (tttt) cc_final: 0.7663 (ttmt) REVERT: L 117 ASN cc_start: 0.8848 (m-40) cc_final: 0.8401 (m110) REVERT: L 135 GLU cc_start: 0.8513 (mp0) cc_final: 0.8221 (mp0) REVERT: L 148 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8538 (mt-10) REVERT: L 150 MET cc_start: 0.8163 (mmp) cc_final: 0.7882 (mmp) REVERT: L 172 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7767 (p0) REVERT: M 42 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8560 (t0) REVERT: M 51 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8991 (mp) REVERT: M 63 TYR cc_start: 0.6746 (m-10) cc_final: 0.6463 (m-80) REVERT: M 89 GLN cc_start: 0.7101 (pt0) cc_final: 0.6839 (pt0) REVERT: M 119 GLU cc_start: 0.7892 (mp0) cc_final: 0.7479 (mp0) REVERT: M 163 GLU cc_start: 0.8460 (mp0) cc_final: 0.8202 (pm20) REVERT: M 167 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7769 (ptm-80) REVERT: M 169 THR cc_start: 0.8500 (m) cc_final: 0.8290 (t) REVERT: M 170 ASP cc_start: 0.8383 (t70) cc_final: 0.7545 (m-30) REVERT: M 190 ILE cc_start: 0.8042 (pt) cc_final: 0.7581 (tt) REVERT: N 1 MET cc_start: 0.3190 (mpp) cc_final: 0.1869 (tmm) REVERT: N 23 ARG cc_start: 0.8945 (tpp-160) cc_final: 0.8734 (tpp-160) REVERT: N 26 LYS cc_start: 0.7550 (tttp) cc_final: 0.7052 (tmtt) REVERT: N 61 PHE cc_start: 0.7445 (m-80) cc_final: 0.7136 (m-10) REVERT: N 137 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7308 (tm-30) REVERT: N 141 ARG cc_start: 0.7621 (ptp-110) cc_final: 0.7362 (ptp-110) REVERT: N 145 LYS cc_start: 0.8712 (mttt) cc_final: 0.8152 (mmtm) REVERT: N 147 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8349 (pttp) REVERT: N 150 MET cc_start: 0.8940 (tpp) cc_final: 0.8535 (tpt) REVERT: N 157 LYS cc_start: 0.8630 (mptt) cc_final: 0.8350 (mttp) REVERT: N 167 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8226 (mtp-110) REVERT: N 172 ASP cc_start: 0.7539 (p0) cc_final: 0.7279 (p0) outliers start: 87 outliers final: 63 residues processed: 800 average time/residue: 0.1453 time to fit residues: 175.9183 Evaluate side-chains 779 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 705 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 114 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 198 optimal weight: 0.0070 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 247 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 132 GLN B 187 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN F 164 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 ASN K 47 GLN ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 65 ASN M 117 ASN ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 GLN N 178 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096580 restraints weight = 49715.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099318 restraints weight = 27793.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101276 restraints weight = 17756.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102678 restraints weight = 12339.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103666 restraints weight = 9188.362| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20457 Z= 0.175 Angle : 0.790 11.938 27624 Z= 0.401 Chirality : 0.049 0.327 3206 Planarity : 0.005 0.054 3597 Dihedral : 5.642 87.706 2784 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 4.15 % Allowed : 29.30 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2562 helix: 0.13 (0.14), residues: 1380 sheet: -0.97 (0.33), residues: 257 loop : -1.62 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 145 TYR 0.025 0.002 TYR E 104 PHE 0.024 0.002 PHE K 50 TRP 0.015 0.003 TRP G 174 HIS 0.016 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00408 (20456) covalent geometry : angle 0.79003 (27624) hydrogen bonds : bond 0.03426 ( 977) hydrogen bonds : angle 4.87620 ( 2865) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 723 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8294 (t70) cc_final: 0.7780 (t-170) REVERT: A 132 GLN cc_start: 0.8932 (mt0) cc_final: 0.7972 (tt0) REVERT: A 167 LYS cc_start: 0.8679 (pttp) cc_final: 0.8332 (pttp) REVERT: B 78 HIS cc_start: 0.7915 (t70) cc_final: 0.7575 (t70) REVERT: B 139 GLU cc_start: 0.8090 (tt0) cc_final: 0.7857 (tm-30) REVERT: B 142 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7077 (tt0) REVERT: C 89 LYS cc_start: 0.6304 (mttt) cc_final: 0.6003 (mttm) REVERT: C 95 TRP cc_start: 0.7272 (p90) cc_final: 0.6832 (p90) REVERT: C 119 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7080 (mtp180) REVERT: C 132 GLN cc_start: 0.8467 (mt0) cc_final: 0.8252 (mt0) REVERT: D 43 GLU cc_start: 0.8655 (tp30) cc_final: 0.8431 (tp30) REVERT: D 47 LYS cc_start: 0.8224 (tttt) cc_final: 0.7586 (ttmm) REVERT: D 79 ASP cc_start: 0.8498 (m-30) cc_final: 0.8216 (m-30) REVERT: D 121 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6783 (ttm) REVERT: D 124 GLN cc_start: 0.8662 (pm20) cc_final: 0.8246 (pm20) REVERT: D 170 ASP cc_start: 0.8296 (p0) cc_final: 0.7979 (m-30) REVERT: E 43 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6809 (tm-30) REVERT: E 47 LYS cc_start: 0.7072 (tttt) cc_final: 0.6226 (tttt) REVERT: E 124 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: F 48 GLN cc_start: 0.8556 (mm110) cc_final: 0.8328 (mp10) REVERT: F 70 HIS cc_start: 0.7953 (t-90) cc_final: 0.7622 (t70) REVERT: F 132 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7791 (mm-40) REVERT: F 136 ILE cc_start: 0.9342 (mm) cc_final: 0.9106 (mm) REVERT: F 137 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7776 (tm-30) REVERT: G 23 GLN cc_start: 0.7328 (tm-30) cc_final: 0.6862 (tm-30) REVERT: G 121 MET cc_start: 0.8220 (tpp) cc_final: 0.7851 (mmm) REVERT: H 38 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6896 (t0) REVERT: H 39 ASN cc_start: 0.8144 (m-40) cc_final: 0.7759 (m-40) REVERT: H 47 GLN cc_start: 0.8862 (mt0) cc_final: 0.8533 (mt0) REVERT: H 78 TYR cc_start: 0.8762 (t80) cc_final: 0.8330 (t80) REVERT: H 85 LYS cc_start: 0.7725 (tptt) cc_final: 0.7096 (tppt) REVERT: H 87 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7414 (t70) REVERT: H 121 MET cc_start: 0.7704 (tmm) cc_final: 0.7479 (tmm) REVERT: H 183 TYR cc_start: 0.7329 (t80) cc_final: 0.6857 (t80) REVERT: I 1 MET cc_start: 0.4488 (mpp) cc_final: 0.2481 (ttt) REVERT: I 18 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5162 (p90) REVERT: I 23 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7600 (tpp-160) REVERT: I 65 ASN cc_start: 0.8271 (t0) cc_final: 0.7145 (t0) REVERT: I 89 GLN cc_start: 0.8102 (mp10) cc_final: 0.7825 (mp10) REVERT: I 113 PHE cc_start: 0.7805 (m-80) cc_final: 0.7572 (m-80) REVERT: I 119 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5579 (mm-30) REVERT: I 160 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7536 (mp10) REVERT: I 163 GLU cc_start: 0.7378 (mp0) cc_final: 0.7004 (pm20) REVERT: J 1 MET cc_start: 0.3429 (ttt) cc_final: 0.3031 (ttt) REVERT: J 70 SER cc_start: 0.8927 (t) cc_final: 0.8360 (m) REVERT: J 151 ASN cc_start: 0.8196 (m-40) cc_final: 0.7921 (m-40) REVERT: J 167 ARG cc_start: 0.8783 (ptm-80) cc_final: 0.8241 (ptm-80) REVERT: K 18 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5557 (p90) REVERT: K 26 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: K 42 ASN cc_start: 0.8576 (t0) cc_final: 0.8093 (t0) REVERT: K 49 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8131 (mm) REVERT: K 65 ASN cc_start: 0.7681 (t0) cc_final: 0.7414 (t0) REVERT: K 95 MET cc_start: 0.8235 (ttp) cc_final: 0.7851 (ttm) REVERT: K 137 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8215 (tm-30) REVERT: K 141 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7787 (mtm110) REVERT: K 148 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8341 (pp20) REVERT: K 190 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6148 (pt) REVERT: L 23 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7552 (tpt90) REVERT: L 32 LEU cc_start: 0.8867 (tp) cc_final: 0.8579 (tt) REVERT: L 39 ASN cc_start: 0.8806 (t0) cc_final: 0.8565 (t0) REVERT: L 85 LYS cc_start: 0.8025 (tttt) cc_final: 0.7589 (ttmt) REVERT: L 135 GLU cc_start: 0.8541 (mp0) cc_final: 0.8276 (mp0) REVERT: L 148 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8442 (mt-10) REVERT: L 150 MET cc_start: 0.8079 (mmp) cc_final: 0.7281 (mmp) REVERT: L 172 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7746 (p0) REVERT: M 63 TYR cc_start: 0.6753 (m-10) cc_final: 0.6538 (m-80) REVERT: M 89 GLN cc_start: 0.7169 (pt0) cc_final: 0.6938 (pt0) REVERT: M 119 GLU cc_start: 0.7802 (mp0) cc_final: 0.7380 (mp0) REVERT: M 149 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8068 (ttp80) REVERT: M 167 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8126 (ttp-110) REVERT: M 169 THR cc_start: 0.8432 (m) cc_final: 0.8217 (t) REVERT: M 170 ASP cc_start: 0.8556 (t70) cc_final: 0.7774 (m-30) REVERT: M 175 MET cc_start: 0.7571 (pmm) cc_final: 0.7146 (pmm) REVERT: M 190 ILE cc_start: 0.8084 (pt) cc_final: 0.7615 (tt) REVERT: N 1 MET cc_start: 0.3462 (mpp) cc_final: 0.1964 (tmm) REVERT: N 26 LYS cc_start: 0.7580 (tttp) cc_final: 0.7023 (tmtt) REVERT: N 61 PHE cc_start: 0.7487 (m-80) cc_final: 0.7282 (m-10) REVERT: N 137 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7321 (tm-30) REVERT: N 141 ARG cc_start: 0.7617 (ptp-110) cc_final: 0.7372 (ptp-110) REVERT: N 145 LYS cc_start: 0.8757 (mttt) cc_final: 0.8317 (mmtm) REVERT: N 147 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8463 (pttp) REVERT: N 167 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8227 (mtp-110) REVERT: N 178 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8186 (pp30) outliers start: 90 outliers final: 67 residues processed: 760 average time/residue: 0.1417 time to fit residues: 163.8980 Evaluate side-chains 762 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 683 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 47 GLN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 242 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 89 GLN I 42 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN M 65 ASN ** M 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098085 restraints weight = 49765.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100883 restraints weight = 27678.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102867 restraints weight = 17476.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104267 restraints weight = 12087.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105092 restraints weight = 8964.639| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20457 Z= 0.158 Angle : 0.821 12.353 27624 Z= 0.413 Chirality : 0.050 0.356 3206 Planarity : 0.005 0.055 3597 Dihedral : 5.599 87.082 2784 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 3.37 % Allowed : 30.92 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2562 helix: 0.11 (0.14), residues: 1379 sheet: -0.85 (0.33), residues: 259 loop : -1.55 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 145 TYR 0.024 0.002 TYR E 104 PHE 0.025 0.002 PHE K 50 TRP 0.091 0.004 TRP G 174 HIS 0.016 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00375 (20456) covalent geometry : angle 0.82092 (27624) hydrogen bonds : bond 0.03445 ( 977) hydrogen bonds : angle 4.85937 ( 2865) Misc. bond : bond 0.00025 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 724 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8217 (t70) cc_final: 0.7698 (t-170) REVERT: A 132 GLN cc_start: 0.8841 (mt0) cc_final: 0.7975 (tt0) REVERT: A 167 LYS cc_start: 0.8654 (pttp) cc_final: 0.8298 (pttp) REVERT: B 63 PHE cc_start: 0.8637 (m-80) cc_final: 0.8422 (m-10) REVERT: B 78 HIS cc_start: 0.7880 (t70) cc_final: 0.7508 (t70) REVERT: B 121 MET cc_start: 0.8292 (tmm) cc_final: 0.7435 (mmm) REVERT: B 139 GLU cc_start: 0.8065 (tt0) cc_final: 0.7856 (tp30) REVERT: C 89 LYS cc_start: 0.6303 (mttt) cc_final: 0.6011 (mttm) REVERT: C 119 ARG cc_start: 0.7678 (mtm180) cc_final: 0.7234 (mtp180) REVERT: C 132 GLN cc_start: 0.8498 (mt0) cc_final: 0.8026 (mt0) REVERT: D 39 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7603 (mt0) REVERT: D 43 GLU cc_start: 0.8590 (tp30) cc_final: 0.8368 (tp30) REVERT: D 47 LYS cc_start: 0.8115 (tttt) cc_final: 0.7510 (ttmm) REVERT: D 79 ASP cc_start: 0.8476 (m-30) cc_final: 0.8185 (m-30) REVERT: D 121 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6619 (ttm) REVERT: D 124 GLN cc_start: 0.8628 (pm20) cc_final: 0.8049 (pm20) REVERT: E 43 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6799 (tm-30) REVERT: E 47 LYS cc_start: 0.7033 (tttt) cc_final: 0.6368 (tttt) REVERT: E 113 PHE cc_start: 0.7766 (m-10) cc_final: 0.7486 (m-10) REVERT: E 153 LEU cc_start: 0.8847 (tt) cc_final: 0.8428 (mt) REVERT: F 24 LYS cc_start: 0.6685 (mmtm) cc_final: 0.6422 (mmtp) REVERT: F 48 GLN cc_start: 0.8510 (mm110) cc_final: 0.8290 (mp10) REVERT: F 70 HIS cc_start: 0.7940 (t-90) cc_final: 0.7564 (t70) REVERT: F 132 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7920 (mm-40) REVERT: F 136 ILE cc_start: 0.9305 (mm) cc_final: 0.9075 (mm) REVERT: F 137 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7775 (tm-30) REVERT: G 23 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6905 (tm-30) REVERT: G 167 LYS cc_start: 0.8876 (ptpp) cc_final: 0.8656 (ptpp) REVERT: H 38 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.6922 (t0) REVERT: H 39 ASN cc_start: 0.8217 (m-40) cc_final: 0.7857 (m-40) REVERT: H 47 GLN cc_start: 0.8828 (mt0) cc_final: 0.8564 (mt0) REVERT: H 78 TYR cc_start: 0.8764 (t80) cc_final: 0.8287 (t80) REVERT: H 85 LYS cc_start: 0.7750 (tptt) cc_final: 0.7522 (tptt) REVERT: H 87 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7438 (t70) REVERT: H 121 MET cc_start: 0.7679 (tmm) cc_final: 0.7457 (tmm) REVERT: H 154 MET cc_start: 0.8654 (mmt) cc_final: 0.8364 (mmt) REVERT: H 183 TYR cc_start: 0.7294 (t80) cc_final: 0.6800 (t80) REVERT: I 1 MET cc_start: 0.4307 (mpp) cc_final: 0.2748 (ttt) REVERT: I 18 TYR cc_start: 0.5596 (OUTLIER) cc_final: 0.4930 (p90) REVERT: I 65 ASN cc_start: 0.8201 (t0) cc_final: 0.6999 (t0) REVERT: I 89 GLN cc_start: 0.8099 (mp10) cc_final: 0.7516 (mp10) REVERT: I 113 PHE cc_start: 0.7727 (m-80) cc_final: 0.7495 (m-80) REVERT: I 119 GLU cc_start: 0.5881 (mm-30) cc_final: 0.5486 (mm-30) REVERT: I 160 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7409 (mp10) REVERT: I 163 GLU cc_start: 0.7314 (mp0) cc_final: 0.6984 (pm20) REVERT: J 1 MET cc_start: 0.3390 (ttt) cc_final: 0.2987 (ttt) REVERT: J 70 SER cc_start: 0.8705 (t) cc_final: 0.8243 (m) REVERT: J 151 ASN cc_start: 0.8176 (m-40) cc_final: 0.7897 (m-40) REVERT: J 167 ARG cc_start: 0.8726 (ptm-80) cc_final: 0.8182 (ptm-80) REVERT: K 18 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5818 (p90) REVERT: K 26 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8005 (tttt) REVERT: K 42 ASN cc_start: 0.8518 (t0) cc_final: 0.8054 (t0) REVERT: K 65 ASN cc_start: 0.7555 (t0) cc_final: 0.7295 (t0) REVERT: K 95 MET cc_start: 0.8136 (ttp) cc_final: 0.7746 (ttm) REVERT: K 137 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8506 (tm-30) REVERT: K 190 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5993 (pt) REVERT: L 23 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7512 (tpt90) REVERT: L 32 LEU cc_start: 0.8858 (tp) cc_final: 0.8638 (tt) REVERT: L 39 ASN cc_start: 0.8852 (t0) cc_final: 0.8557 (t0) REVERT: L 85 LYS cc_start: 0.8042 (tttt) cc_final: 0.7602 (ttmt) REVERT: L 135 GLU cc_start: 0.8491 (mp0) cc_final: 0.8263 (mp0) REVERT: L 172 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7611 (p0) REVERT: M 23 ARG cc_start: 0.8094 (tpt90) cc_final: 0.7384 (tpm170) REVERT: M 89 GLN cc_start: 0.7215 (pt0) cc_final: 0.7002 (pt0) REVERT: M 119 GLU cc_start: 0.7923 (mp0) cc_final: 0.7503 (mp0) REVERT: M 149 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8121 (ttp80) REVERT: M 167 ARG cc_start: 0.8316 (ttp-110) cc_final: 0.7851 (ptm-80) REVERT: M 170 ASP cc_start: 0.8622 (t70) cc_final: 0.7596 (m-30) REVERT: M 175 MET cc_start: 0.7356 (pmm) cc_final: 0.7083 (pmm) REVERT: M 190 ILE cc_start: 0.8009 (pt) cc_final: 0.7525 (tt) REVERT: N 1 MET cc_start: 0.3507 (mpp) cc_final: 0.2020 (tmm) REVERT: N 26 LYS cc_start: 0.7648 (tttp) cc_final: 0.7083 (tmtt) REVERT: N 145 LYS cc_start: 0.8700 (mttt) cc_final: 0.8228 (mmtm) REVERT: N 147 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8448 (pttp) REVERT: N 148 GLU cc_start: 0.8683 (pt0) cc_final: 0.8427 (pt0) REVERT: N 167 ARG cc_start: 0.8382 (mtm110) cc_final: 0.8149 (ptp90) REVERT: N 178 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (pp30) REVERT: N 183 TYR cc_start: 0.8086 (t80) cc_final: 0.7235 (t80) outliers start: 73 outliers final: 58 residues processed: 758 average time/residue: 0.1440 time to fit residues: 166.3112 Evaluate side-chains 752 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 684 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 78 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN I 42 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097915 restraints weight = 49443.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100764 restraints weight = 27461.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102759 restraints weight = 17358.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.104182 restraints weight = 11970.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105169 restraints weight = 8833.044| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.233 20457 Z= 0.316 Angle : 1.131 59.200 27624 Z= 0.633 Chirality : 0.061 1.887 3206 Planarity : 0.005 0.108 3597 Dihedral : 5.596 87.079 2784 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 3.74 % Allowed : 30.96 % Favored : 65.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2562 helix: 0.10 (0.14), residues: 1379 sheet: -0.80 (0.33), residues: 259 loop : -1.56 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG N 28 TYR 0.051 0.002 TYR M 63 PHE 0.027 0.002 PHE B 63 TRP 0.092 0.007 TRP F 174 HIS 0.019 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00727 (20456) covalent geometry : angle 1.13107 (27624) hydrogen bonds : bond 0.03471 ( 977) hydrogen bonds : angle 4.86320 ( 2865) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.84 seconds wall clock time: 66 minutes 18.42 seconds (3978.42 seconds total)