Starting phenix.real_space_refine on Sun Aug 24 06:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2u_28827/08_2025/8f2u_28827.map" } resolution = 3.53 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= -0.000 sd= 0.003 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 77 5.16 5 C 11198 2.51 5 N 3076 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17684 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1466 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "B" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1601 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "C" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1555 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1520 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "E" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1598 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1583 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "H" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1449 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "I" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "J" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1589 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "N" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "T" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1364 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 156} Time building chain proxies: 3.92, per 1000 atoms: 0.22 Number of scatterers: 17684 At special positions: 0 Unit cell: (117.072, 137.668, 132.248, 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 77 16.00 O 3333 8.00 N 3076 7.00 C 11198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 865.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 5 sheets defined 62.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.950A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.673A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 4.360A pdb=" N ALA A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.797A pdb=" N LYS A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.722A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.736A pdb=" N GLU B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.580A pdb=" N GLU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.589A pdb=" N VAL B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.575A pdb=" N ASN B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.858A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.567A pdb=" N LYS B 187 " --> pdb=" O GLU B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.695A pdb=" N ILE B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.580A pdb=" N ALA C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.574A pdb=" N VAL C 45 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.714A pdb=" N ASN C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.619A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.612A pdb=" N LEU D 16 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.770A pdb=" N SER D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 61 through 82 removed outlier: 3.787A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.510A pdb=" N SER D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.880A pdb=" N CYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 177 through 196 Processing helix chain 'E' and resid 30 through 40 removed outlier: 4.001A pdb=" N ARG E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.626A pdb=" N PHE E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.617A pdb=" N VAL E 68 " --> pdb=" O CYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 removed outlier: 3.669A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 105 through 113 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 134 through 144 Processing helix chain 'E' and resid 193 through 221 removed outlier: 3.973A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.301A pdb=" N LEU G 22 " --> pdb=" O MET G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 Processing helix chain 'G' and resid 47 through 62 removed outlier: 3.815A pdb=" N LEU G 51 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.748A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 86 Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 102 through 127 removed outlier: 3.995A pdb=" N TYR G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Proline residue: G 118 - end of helix removed outlier: 3.750A pdb=" N ILE G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY G 126 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 127 " --> pdb=" O TRP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 197 removed outlier: 3.589A pdb=" N GLU G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.951A pdb=" N ARG H 11 " --> pdb=" O PRO H 8 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN H 13 " --> pdb=" O TRP H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.970A pdb=" N LEU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.507A pdb=" N ASP H 41 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS H 43 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR H 44 " --> pdb=" O ASP H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 69 removed outlier: 4.062A pdb=" N HIS H 53 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 3.763A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.529A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 183 removed outlier: 3.769A pdb=" N VAL H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 18 removed outlier: 3.762A pdb=" N LYS I 17 " --> pdb=" O SER I 14 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 18 " --> pdb=" O LEU I 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 18' Processing helix chain 'I' and resid 20 through 32 removed outlier: 4.141A pdb=" N VAL I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 3.534A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 51 " --> pdb=" O CYS I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 removed outlier: 3.943A pdb=" N ALA I 57 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 84 removed outlier: 3.603A pdb=" N ILE I 82 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 105 removed outlier: 3.968A pdb=" N LEU I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS I 105 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 114 removed outlier: 3.874A pdb=" N TRP I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 removed outlier: 3.788A pdb=" N CYS I 160 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 198 Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 29 through 39 removed outlier: 4.653A pdb=" N LEU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 38 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.707A pdb=" N LEU J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.633A pdb=" N LEU J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU J 97 " --> pdb=" O GLN J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 102 through 126 removed outlier: 6.019A pdb=" N GLN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 120 " --> pdb=" O MET J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 199 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'N' and resid 24 through 36 removed outlier: 4.176A pdb=" N GLU N 29 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 48 through 64 removed outlier: 3.815A pdb=" N LYS N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 62 " --> pdb=" O THR N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 94 removed outlier: 4.777A pdb=" N ALA N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 98 Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.323A pdb=" N GLN N 109 " --> pdb=" O PRO N 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 Proline residue: N 118 - end of helix removed outlier: 3.780A pdb=" N GLN N 121 " --> pdb=" O PHE N 117 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP N 122 " --> pdb=" O PRO N 118 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 123 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU N 132 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 150 removed outlier: 4.466A pdb=" N THR N 149 " --> pdb=" O GLN N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 176 removed outlier: 3.846A pdb=" N ASP N 157 " --> pdb=" O PRO N 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE N 158 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS N 160 " --> pdb=" O ASP N 156 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS N 164 " --> pdb=" O LYS N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.867A pdb=" N HIS N 199 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 203 " --> pdb=" O HIS N 199 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU N 204 " --> pdb=" O ALA N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 278 Processing helix chain 'N' and resid 278 through 301 removed outlier: 5.970A pdb=" N ALA N 284 " --> pdb=" O GLY N 280 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU N 285 " --> pdb=" O LEU N 281 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER N 298 " --> pdb=" O ALA N 294 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU N 299 " --> pdb=" O GLU N 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 140 removed outlier: 4.425A pdb=" N LEU T 127 " --> pdb=" O SER T 123 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 140 " --> pdb=" O ASP T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 148 Processing helix chain 'T' and resid 149 through 156 Processing helix chain 'T' and resid 178 through 185 removed outlier: 3.786A pdb=" N GLU T 182 " --> pdb=" O GLY T 178 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE T 183 " --> pdb=" O GLU T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 195 Processing helix chain 'T' and resid 198 through 219 Processing helix chain 'T' and resid 230 through 235 removed outlier: 4.173A pdb=" N LEU T 235 " --> pdb=" O THR T 232 " (cutoff:3.500A) Processing helix chain 'T' and resid 241 through 258 removed outlier: 3.937A pdb=" N ARG T 247 " --> pdb=" O ALA T 243 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU T 248 " --> pdb=" O GLN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 280 removed outlier: 4.069A pdb=" N ALA T 278 " --> pdb=" O GLU T 274 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP T 279 " --> pdb=" O LEU T 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.713A pdb=" N ILE A 145 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 117 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS F 48 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 21 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA F 50 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU F 19 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET F 28 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR D 141 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 30 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP D 139 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER F 32 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG D 137 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 133 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 152 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 161 " --> pdb=" O GLN D 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.713A pdb=" N ILE A 145 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP A 124 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER I 136 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 126 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL I 130 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 132 " --> pdb=" O TRP I 128 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP I 128 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU I 123 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN I 154 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP I 125 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS I 147 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 167 removed outlier: 3.870A pdb=" N ASN B 126 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN B 155 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR B 124 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TRP B 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER H 130 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 131 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL H 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER B 137 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP H 122 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU H 117 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS H 148 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP H 119 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 removed outlier: 3.835A pdb=" N ASP C 127 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 156 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 125 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 146 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR C 134 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN J 144 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 136 " --> pdb=" O ASN J 142 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN J 142 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR C 138 " --> pdb=" O GLN J 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN J 140 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY J 163 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL J 137 " --> pdb=" O GLN J 161 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLN J 161 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP J 139 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL J 159 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU J 141 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN J 157 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU J 143 " --> pdb=" O SER J 155 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER J 155 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.702A pdb=" N VAL E 176 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 181 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 154 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG E 158 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER G 147 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP E 160 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER G 145 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA E 162 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL G 143 " --> pdb=" O ALA E 162 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN G 133 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL G 163 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET G 137 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS G 161 " --> pdb=" O MET G 137 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP G 139 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN G 159 " --> pdb=" O TRP G 139 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE G 141 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE G 157 " --> pdb=" O PHE G 141 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5898 1.34 - 1.46: 3571 1.46 - 1.58: 8398 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 17989 Sorted by residual: bond pdb=" N GLY E 20 " pdb=" CA GLY E 20 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.23e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N GLN N 23 " pdb=" CA GLN N 23 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N GLU H 5 " pdb=" CA GLU H 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 17984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 24209 3.20 - 6.40: 86 6.40 - 9.60: 2 9.60 - 12.80: 3 12.80 - 16.00: 1 Bond angle restraints: 24301 Sorted by residual: angle pdb=" C LEU E 113 " pdb=" N GLN E 114 " pdb=" CA GLN E 114 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 angle pdb=" CG1 ILE J 8 " pdb=" CB ILE J 8 " pdb=" CG2 ILE J 8 " ideal model delta sigma weight residual 110.70 126.70 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" CA ILE J 99 " pdb=" CB ILE J 99 " pdb=" CG2 ILE J 99 " ideal model delta sigma weight residual 110.50 118.27 -7.77 1.70e+00 3.46e-01 2.09e+01 angle pdb=" N GLU E 115 " pdb=" CA GLU E 115 " pdb=" C GLU E 115 " ideal model delta sigma weight residual 111.75 116.79 -5.04 1.28e+00 6.10e-01 1.55e+01 angle pdb=" CG1 ILE J 99 " pdb=" CB ILE J 99 " pdb=" CG2 ILE J 99 " ideal model delta sigma weight residual 110.70 122.45 -11.75 3.00e+00 1.11e-01 1.53e+01 ... (remaining 24296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9892 17.97 - 35.93: 942 35.93 - 53.90: 170 53.90 - 71.86: 49 71.86 - 89.83: 34 Dihedral angle restraints: 11087 sinusoidal: 4552 harmonic: 6535 Sorted by residual: dihedral pdb=" C LEU E 113 " pdb=" N LEU E 113 " pdb=" CA LEU E 113 " pdb=" CB LEU E 113 " ideal model delta harmonic sigma weight residual -122.60 -132.01 9.41 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C GLU E 115 " pdb=" N GLU E 115 " pdb=" CA GLU E 115 " pdb=" CB GLU E 115 " ideal model delta harmonic sigma weight residual -122.60 -131.78 9.18 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N GLU E 115 " pdb=" C GLU E 115 " pdb=" CA GLU E 115 " pdb=" CB GLU E 115 " ideal model delta harmonic sigma weight residual 122.80 131.98 -9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 11084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 2787 0.335 - 0.669: 4 0.669 - 1.004: 0 1.004 - 1.338: 0 1.338 - 1.673: 3 Chirality restraints: 2794 Sorted by residual: chirality pdb=" CB ILE J 8 " pdb=" CA ILE J 8 " pdb=" CG1 ILE J 8 " pdb=" CG2 ILE J 8 " both_signs ideal model delta sigma weight residual False 2.64 0.97 1.67 2.00e-01 2.50e+01 7.00e+01 chirality pdb=" CG LEU J 68 " pdb=" CB LEU J 68 " pdb=" CD1 LEU J 68 " pdb=" CD2 LEU J 68 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.65 2.00e-01 2.50e+01 6.81e+01 chirality pdb=" CB ILE J 99 " pdb=" CA ILE J 99 " pdb=" CG1 ILE J 99 " pdb=" CG2 ILE J 99 " both_signs ideal model delta sigma weight residual False 2.64 1.17 1.47 2.00e-01 2.50e+01 5.40e+01 ... (remaining 2791 not shown) Planarity restraints: 3119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 118 " -0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO E 119 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 119 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 119 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 117 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO G 118 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 118 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 118 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU T 235 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO T 236 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO T 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO T 236 " -0.028 5.00e-02 4.00e+02 ... (remaining 3116 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 126 2.57 - 3.15: 14415 3.15 - 3.73: 26301 3.73 - 4.32: 34214 4.32 - 4.90: 58647 Nonbonded interactions: 133703 Sorted by model distance: nonbonded pdb=" OD1 ASN G 23 " pdb=" OG SER G 102 " model vdw 1.983 3.040 nonbonded pdb=" OH TYR J 188 " pdb=" OG1 THR N 201 " model vdw 1.983 3.040 nonbonded pdb=" O PHE D 5 " pdb=" OG SER D 78 " model vdw 2.078 3.040 nonbonded pdb=" O GLU D 18 " pdb=" OG1 THR D 21 " model vdw 2.086 3.040 nonbonded pdb=" OG SER H 48 " pdb=" OE1 GLU H 49 " model vdw 2.092 3.040 ... (remaining 133698 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.160 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.002 0.057 17989 Z= 0.120 Angle : 0.560 15.999 24301 Z= 0.310 Chirality : 0.065 1.673 2794 Planarity : 0.004 0.077 3119 Dihedral : 15.519 89.827 6815 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.04 (0.18), residues: 2210 helix: 1.80 (0.15), residues: 1183 sheet: 0.79 (0.33), residues: 269 loop : -1.18 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 110 TYR 0.017 0.001 TYR B 67 PHE 0.014 0.001 PHE G 38 TRP 0.012 0.001 TRP N 59 HIS 0.005 0.001 HIS J 69 Details of bonding type rmsd covalent geometry : bond 0.00245 (17989) covalent geometry : angle 0.56030 (24301) hydrogen bonds : bond 0.17572 ( 1027) hydrogen bonds : angle 6.60588 ( 3009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: C 107 ASN cc_start: 0.7638 (p0) cc_final: 0.7376 (p0) REVERT: D 1 MET cc_start: 0.4009 (ttt) cc_final: 0.3501 (ttt) REVERT: E 111 ASP cc_start: 0.4996 (m-30) cc_final: 0.4551 (m-30) REVERT: E 115 GLU cc_start: 0.5107 (mm-30) cc_final: 0.4166 (pm20) REVERT: F 48 LYS cc_start: 0.7219 (ptmt) cc_final: 0.6909 (mtpt) REVERT: H 88 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5968 (mm-30) REVERT: H 119 ASP cc_start: 0.7247 (p0) cc_final: 0.7039 (p0) REVERT: I 40 LYS cc_start: 0.6663 (tttp) cc_final: 0.5891 (ttmt) REVERT: N 112 ASP cc_start: 0.3312 (m-30) cc_final: 0.3045 (p0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1382 time to fit residues: 48.1218 Evaluate side-chains 164 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN D 102 HIS D 118 GLN D 190 GLN F 52 HIS ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN N 82 GLN T 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.165805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.142238 restraints weight = 32228.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.141546 restraints weight = 48414.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142219 restraints weight = 43790.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.142030 restraints weight = 29246.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142282 restraints weight = 27773.681| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17989 Z= 0.129 Angle : 0.566 7.978 24301 Z= 0.291 Chirality : 0.039 0.186 2794 Planarity : 0.004 0.056 3119 Dihedral : 4.003 18.011 2380 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.97 % Allowed : 6.73 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.03 (0.18), residues: 2210 helix: 1.69 (0.15), residues: 1220 sheet: 0.72 (0.31), residues: 283 loop : -1.14 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 127 TYR 0.011 0.001 TYR C 86 PHE 0.031 0.001 PHE D 5 TRP 0.019 0.001 TRP G 123 HIS 0.011 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00270 (17989) covalent geometry : angle 0.56579 (24301) hydrogen bonds : bond 0.04202 ( 1027) hydrogen bonds : angle 4.78695 ( 3009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.739 Fit side-chains REVERT: C 144 MET cc_start: 0.6651 (mtm) cc_final: 0.6413 (mtm) REVERT: D 1 MET cc_start: 0.4052 (ttt) cc_final: 0.3647 (ttt) REVERT: E 115 GLU cc_start: 0.5609 (mm-30) cc_final: 0.4311 (pm20) REVERT: F 48 LYS cc_start: 0.7469 (ptmt) cc_final: 0.7181 (mtpt) REVERT: H 91 MET cc_start: 0.6674 (mpp) cc_final: 0.6318 (mpp) REVERT: H 119 ASP cc_start: 0.7405 (p0) cc_final: 0.7161 (p0) REVERT: J 75 ILE cc_start: 0.7576 (mm) cc_final: 0.7149 (mt) REVERT: N 160 LYS cc_start: 0.6718 (mtmm) cc_final: 0.5957 (tptp) REVERT: N 287 LYS cc_start: 0.3837 (ttmt) cc_final: 0.3414 (tppt) outliers start: 19 outliers final: 13 residues processed: 189 average time/residue: 0.1432 time to fit residues: 40.9241 Evaluate side-chains 163 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN C 76 HIS C 106 ASN F 52 HIS ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 147 GLN T 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.162920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.140154 restraints weight = 32793.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140700 restraints weight = 58329.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.140812 restraints weight = 50560.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140847 restraints weight = 32699.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.141116 restraints weight = 29145.509| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17989 Z= 0.154 Angle : 0.568 8.638 24301 Z= 0.291 Chirality : 0.039 0.147 2794 Planarity : 0.004 0.046 3119 Dihedral : 4.056 18.003 2380 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.22 % Allowed : 10.24 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 0.77 (0.18), residues: 2210 helix: 1.46 (0.15), residues: 1226 sheet: 0.54 (0.30), residues: 296 loop : -1.22 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 127 TYR 0.010 0.001 TYR N 176 PHE 0.022 0.002 PHE J 30 TRP 0.013 0.001 TRP A 98 HIS 0.011 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00347 (17989) covalent geometry : angle 0.56790 (24301) hydrogen bonds : bond 0.04209 ( 1027) hydrogen bonds : angle 4.57602 ( 3009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: E 115 GLU cc_start: 0.5694 (mm-30) cc_final: 0.4288 (pm20) REVERT: F 48 LYS cc_start: 0.7415 (ptmt) cc_final: 0.7119 (mtpt) REVERT: G 1 MET cc_start: 0.3627 (OUTLIER) cc_final: 0.2827 (ttm) REVERT: G 120 LEU cc_start: 0.4099 (mp) cc_final: 0.3374 (mt) REVERT: H 39 TYR cc_start: 0.5984 (t80) cc_final: 0.5735 (t80) REVERT: H 91 MET cc_start: 0.7004 (mpp) cc_final: 0.6590 (mpp) REVERT: H 119 ASP cc_start: 0.7635 (p0) cc_final: 0.7288 (p0) REVERT: J 44 LYS cc_start: 0.5014 (mmtp) cc_final: 0.4588 (mmtp) REVERT: J 75 ILE cc_start: 0.7633 (mm) cc_final: 0.7280 (mt) REVERT: N 66 PHE cc_start: 0.3864 (OUTLIER) cc_final: 0.2822 (t80) REVERT: N 160 LYS cc_start: 0.6756 (mtmm) cc_final: 0.5969 (tptp) REVERT: N 287 LYS cc_start: 0.4218 (ttmt) cc_final: 0.3788 (tppt) outliers start: 24 outliers final: 15 residues processed: 186 average time/residue: 0.1476 time to fit residues: 41.1371 Evaluate side-chains 170 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 85 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 214 optimal weight: 0.1980 chunk 213 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 ASN D 118 GLN E 95 GLN F 52 HIS G 80 ASN ** I 62 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 = 0.4225 r_free = 0.4225 target = 0.161842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135806 restraints weight = 33107.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134554 restraints weight = 56470.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135548 restraints weight = 54384.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136014 restraints weight = 33417.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.136325 restraints weight = 31156.934| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17989 Z= 0.127 Angle : 0.531 8.928 24301 Z= 0.271 Chirality : 0.038 0.146 2794 Planarity : 0.004 0.048 3119 Dihedral : 3.978 17.350 2380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 11.26 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 0.83 (0.18), residues: 2210 helix: 1.48 (0.15), residues: 1229 sheet: 0.64 (0.30), residues: 289 loop : -1.18 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 127 TYR 0.013 0.001 TYR N 176 PHE 0.020 0.001 PHE D 5 TRP 0.036 0.001 TRP H 51 HIS 0.008 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00287 (17989) covalent geometry : angle 0.53063 (24301) hydrogen bonds : bond 0.03750 ( 1027) hydrogen bonds : angle 4.38072 ( 3009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.540 Fit side-chains REVERT: B 15 PHE cc_start: 0.6009 (t80) cc_final: 0.5755 (t80) REVERT: E 115 GLU cc_start: 0.5679 (mm-30) cc_final: 0.4364 (pm20) REVERT: F 48 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7115 (mtpt) REVERT: G 1 MET cc_start: 0.3303 (OUTLIER) cc_final: 0.2721 (ttm) REVERT: G 120 LEU cc_start: 0.4167 (mp) cc_final: 0.3554 (mt) REVERT: H 91 MET cc_start: 0.7078 (mpp) cc_final: 0.6711 (mpp) REVERT: J 75 ILE cc_start: 0.7947 (mm) cc_final: 0.7594 (mt) REVERT: N 66 PHE cc_start: 0.4023 (OUTLIER) cc_final: 0.2951 (t80) REVERT: N 160 LYS cc_start: 0.6981 (mtmm) cc_final: 0.6131 (tptp) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.1309 time to fit residues: 38.0130 Evaluate side-chains 174 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.3980 chunk 205 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 ASN D 118 GLN F 52 HIS N 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.163002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137715 restraints weight = 32411.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136253 restraints weight = 55535.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137006 restraints weight = 51024.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138535 restraints weight = 33046.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138544 restraints weight = 25010.200| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17989 Z= 0.109 Angle : 0.506 9.006 24301 Z= 0.257 Chirality : 0.037 0.140 2794 Planarity : 0.004 0.047 3119 Dihedral : 3.861 16.757 2380 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 12.54 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.02 (0.18), residues: 2210 helix: 1.66 (0.15), residues: 1226 sheet: 0.78 (0.30), residues: 288 loop : -1.15 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 127 TYR 0.011 0.001 TYR N 176 PHE 0.019 0.001 PHE D 5 TRP 0.019 0.001 TRP H 51 HIS 0.007 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00238 (17989) covalent geometry : angle 0.50592 (24301) hydrogen bonds : bond 0.03441 ( 1027) hydrogen bonds : angle 4.23853 ( 3009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 115 GLU cc_start: 0.5657 (mm-30) cc_final: 0.4324 (pm20) REVERT: F 48 LYS cc_start: 0.7422 (ptmt) cc_final: 0.7085 (mtpt) REVERT: G 1 MET cc_start: 0.3373 (OUTLIER) cc_final: 0.2756 (ttm) REVERT: G 120 LEU cc_start: 0.4306 (mp) cc_final: 0.3673 (mt) REVERT: H 91 MET cc_start: 0.7150 (mpp) cc_final: 0.6780 (mpp) REVERT: I 83 LEU cc_start: 0.3058 (OUTLIER) cc_final: 0.2715 (tt) REVERT: J 75 ILE cc_start: 0.7976 (mm) cc_final: 0.7642 (mt) REVERT: N 64 CYS cc_start: 0.2845 (OUTLIER) cc_final: 0.2640 (t) REVERT: N 66 PHE cc_start: 0.4003 (OUTLIER) cc_final: 0.3058 (t80) REVERT: N 160 LYS cc_start: 0.6937 (mtmm) cc_final: 0.6110 (tptp) outliers start: 30 outliers final: 19 residues processed: 191 average time/residue: 0.1291 time to fit residues: 37.8183 Evaluate side-chains 180 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 64 CYS Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN F 52 HIS I 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135333 restraints weight = 32351.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135083 restraints weight = 59206.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135897 restraints weight = 53477.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136150 restraints weight = 33147.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136578 restraints weight = 30146.135| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17989 Z= 0.142 Angle : 0.541 9.261 24301 Z= 0.275 Chirality : 0.038 0.142 2794 Planarity : 0.004 0.048 3119 Dihedral : 3.997 15.762 2380 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 13.40 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 0.89 (0.18), residues: 2210 helix: 1.52 (0.15), residues: 1229 sheet: 0.70 (0.30), residues: 297 loop : -1.15 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.010 0.001 TYR D 48 PHE 0.017 0.002 PHE D 5 TRP 0.018 0.001 TRP N 59 HIS 0.005 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00327 (17989) covalent geometry : angle 0.54110 (24301) hydrogen bonds : bond 0.03841 ( 1027) hydrogen bonds : angle 4.31077 ( 3009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ILE cc_start: 0.8146 (pt) cc_final: 0.7870 (pt) REVERT: E 115 GLU cc_start: 0.5662 (mm-30) cc_final: 0.4358 (pm20) REVERT: F 48 LYS cc_start: 0.7459 (ptmt) cc_final: 0.7120 (mtpt) REVERT: G 1 MET cc_start: 0.3312 (OUTLIER) cc_final: 0.2782 (ttm) REVERT: H 91 MET cc_start: 0.7197 (mpp) cc_final: 0.6837 (mpp) REVERT: I 83 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2622 (tt) REVERT: J 58 GLN cc_start: 0.5434 (OUTLIER) cc_final: 0.5083 (tm-30) REVERT: J 75 ILE cc_start: 0.8097 (mm) cc_final: 0.7736 (mt) REVERT: N 64 CYS cc_start: 0.2494 (OUTLIER) cc_final: 0.2282 (t) REVERT: N 66 PHE cc_start: 0.4139 (OUTLIER) cc_final: 0.3322 (t80) REVERT: N 160 LYS cc_start: 0.7139 (mtmm) cc_final: 0.6260 (tptp) outliers start: 32 outliers final: 19 residues processed: 193 average time/residue: 0.1283 time to fit residues: 38.3653 Evaluate side-chains 185 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 64 CYS Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 174 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 139 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 199 optimal weight: 0.0470 chunk 84 optimal weight: 7.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 ASN F 52 HIS G 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.162948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137281 restraints weight = 32605.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136086 restraints weight = 53763.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.136811 restraints weight = 49082.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137875 restraints weight = 32600.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137943 restraints weight = 28314.338| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17989 Z= 0.100 Angle : 0.495 9.323 24301 Z= 0.251 Chirality : 0.037 0.132 2794 Planarity : 0.004 0.047 3119 Dihedral : 3.779 14.634 2380 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.48 % Allowed : 13.76 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.16 (0.18), residues: 2210 helix: 1.72 (0.15), residues: 1232 sheet: 0.97 (0.31), residues: 288 loop : -1.08 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 127 TYR 0.010 0.001 TYR C 86 PHE 0.018 0.001 PHE D 5 TRP 0.020 0.001 TRP N 59 HIS 0.004 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00217 (17989) covalent geometry : angle 0.49547 (24301) hydrogen bonds : bond 0.03180 ( 1027) hydrogen bonds : angle 4.10207 ( 3009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 MET cc_start: 0.7695 (mmt) cc_final: 0.7384 (mmt) REVERT: D 51 ILE cc_start: 0.8093 (pt) cc_final: 0.7810 (pt) REVERT: D 196 SER cc_start: 0.8656 (t) cc_final: 0.8397 (m) REVERT: E 115 GLU cc_start: 0.5675 (mm-30) cc_final: 0.4328 (pm20) REVERT: F 48 LYS cc_start: 0.7368 (ptmt) cc_final: 0.7018 (mtpt) REVERT: G 1 MET cc_start: 0.3538 (OUTLIER) cc_final: 0.2973 (ttm) REVERT: G 120 LEU cc_start: 0.4161 (mp) cc_final: 0.3578 (mt) REVERT: H 91 MET cc_start: 0.7115 (mpp) cc_final: 0.6878 (mpp) REVERT: I 54 GLN cc_start: 0.5935 (mm-40) cc_final: 0.5636 (mm-40) REVERT: I 83 LEU cc_start: 0.2881 (OUTLIER) cc_final: 0.2558 (tt) REVERT: J 58 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4842 (tm-30) REVERT: J 75 ILE cc_start: 0.8001 (mm) cc_final: 0.7652 (mt) REVERT: N 66 PHE cc_start: 0.4102 (OUTLIER) cc_final: 0.3375 (t80) REVERT: N 160 LYS cc_start: 0.7017 (mtmm) cc_final: 0.6120 (tptp) outliers start: 29 outliers final: 17 residues processed: 193 average time/residue: 0.1133 time to fit residues: 33.9786 Evaluate side-chains 188 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 2 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS C 106 ASN D 94 GLN F 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.160895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133866 restraints weight = 32339.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132104 restraints weight = 54005.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133354 restraints weight = 47879.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134103 restraints weight = 28780.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134415 restraints weight = 27551.336| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17989 Z= 0.122 Angle : 0.520 9.422 24301 Z= 0.264 Chirality : 0.038 0.154 2794 Planarity : 0.004 0.048 3119 Dihedral : 3.851 14.706 2380 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.43 % Allowed : 14.27 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.09 (0.18), residues: 2210 helix: 1.65 (0.15), residues: 1233 sheet: 0.96 (0.31), residues: 288 loop : -1.09 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.009 0.001 TYR D 48 PHE 0.016 0.001 PHE N 146 TRP 0.021 0.001 TRP N 59 HIS 0.004 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00279 (17989) covalent geometry : angle 0.52003 (24301) hydrogen bonds : bond 0.03475 ( 1027) hydrogen bonds : angle 4.15481 ( 3009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.6474 (tpp) cc_final: 0.5958 (mmt) REVERT: B 186 MET cc_start: 0.7822 (mmt) cc_final: 0.7494 (mmt) REVERT: D 51 ILE cc_start: 0.8071 (pt) cc_final: 0.7795 (pt) REVERT: E 115 GLU cc_start: 0.5609 (mm-30) cc_final: 0.4197 (pm20) REVERT: F 48 LYS cc_start: 0.7434 (ptmt) cc_final: 0.7077 (mtpt) REVERT: G 1 MET cc_start: 0.3318 (OUTLIER) cc_final: 0.2839 (ttm) REVERT: H 91 MET cc_start: 0.7188 (mpp) cc_final: 0.6948 (mpp) REVERT: H 119 ASP cc_start: 0.7901 (p0) cc_final: 0.7459 (p0) REVERT: I 83 LEU cc_start: 0.2991 (OUTLIER) cc_final: 0.2653 (tt) REVERT: J 58 GLN cc_start: 0.5354 (OUTLIER) cc_final: 0.4987 (tm-30) REVERT: J 75 ILE cc_start: 0.8154 (mm) cc_final: 0.7768 (mt) REVERT: N 66 PHE cc_start: 0.4050 (OUTLIER) cc_final: 0.3329 (t80) REVERT: N 160 LYS cc_start: 0.7166 (mtmm) cc_final: 0.6208 (tptp) outliers start: 28 outliers final: 19 residues processed: 189 average time/residue: 0.1165 time to fit residues: 34.5339 Evaluate side-chains 189 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 186 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 214 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN C 48 HIS C 76 HIS C 106 ASN F 52 HIS T 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134464 restraints weight = 32538.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133252 restraints weight = 53407.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134304 restraints weight = 47446.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134800 restraints weight = 28335.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135120 restraints weight = 26830.780| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17989 Z= 0.115 Angle : 0.511 9.474 24301 Z= 0.259 Chirality : 0.037 0.150 2794 Planarity : 0.004 0.048 3119 Dihedral : 3.818 17.995 2380 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.38 % Allowed : 14.68 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 1.10 (0.18), residues: 2210 helix: 1.65 (0.15), residues: 1236 sheet: 1.00 (0.31), residues: 288 loop : -1.10 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 127 TYR 0.010 0.001 TYR D 48 PHE 0.018 0.001 PHE N 146 TRP 0.021 0.001 TRP N 59 HIS 0.003 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00258 (17989) covalent geometry : angle 0.51141 (24301) hydrogen bonds : bond 0.03347 ( 1027) hydrogen bonds : angle 4.12005 ( 3009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.6469 (tpp) cc_final: 0.5919 (mmt) REVERT: B 186 MET cc_start: 0.7846 (mmt) cc_final: 0.7565 (mmt) REVERT: D 51 ILE cc_start: 0.8080 (pt) cc_final: 0.7800 (pt) REVERT: E 115 GLU cc_start: 0.5672 (mm-30) cc_final: 0.4308 (pm20) REVERT: F 48 LYS cc_start: 0.7438 (ptmt) cc_final: 0.7082 (mtpt) REVERT: G 1 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.3019 (ttm) REVERT: H 91 MET cc_start: 0.7169 (mpp) cc_final: 0.6919 (mpp) REVERT: H 119 ASP cc_start: 0.7818 (p0) cc_final: 0.7420 (p0) REVERT: I 83 LEU cc_start: 0.3275 (OUTLIER) cc_final: 0.2915 (tt) REVERT: J 58 GLN cc_start: 0.5384 (OUTLIER) cc_final: 0.4925 (tm-30) REVERT: J 75 ILE cc_start: 0.8146 (mm) cc_final: 0.7775 (mt) REVERT: N 66 PHE cc_start: 0.3995 (OUTLIER) cc_final: 0.3296 (t80) REVERT: N 111 MET cc_start: 0.1009 (mmm) cc_final: 0.0793 (mmm) REVERT: N 160 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6287 (tptp) outliers start: 27 outliers final: 21 residues processed: 194 average time/residue: 0.1249 time to fit residues: 37.8367 Evaluate side-chains 187 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN C 106 ASN F 52 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.157987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.134901 restraints weight = 32505.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134329 restraints weight = 59661.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134971 restraints weight = 52024.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135008 restraints weight = 31892.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135544 restraints weight = 28733.814| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17989 Z= 0.200 Angle : 0.625 9.859 24301 Z= 0.317 Chirality : 0.041 0.185 2794 Planarity : 0.005 0.048 3119 Dihedral : 4.274 15.569 2380 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.53 % Allowed : 14.78 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 0.54 (0.18), residues: 2210 helix: 1.22 (0.15), residues: 1234 sheet: 0.63 (0.31), residues: 297 loop : -1.34 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 137 TYR 0.019 0.002 TYR B 103 PHE 0.020 0.002 PHE C 168 TRP 0.024 0.002 TRP N 59 HIS 0.006 0.001 HIS I 65 Details of bonding type rmsd covalent geometry : bond 0.00473 (17989) covalent geometry : angle 0.62544 (24301) hydrogen bonds : bond 0.04435 ( 1027) hydrogen bonds : angle 4.47968 ( 3009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: C 172 MET cc_start: 0.6979 (ttt) cc_final: 0.6738 (ttt) REVERT: D 51 ILE cc_start: 0.8139 (pt) cc_final: 0.7862 (pt) REVERT: E 115 GLU cc_start: 0.5610 (mm-30) cc_final: 0.4951 (tt0) REVERT: F 48 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7109 (mtpt) REVERT: G 1 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.3191 (ttm) REVERT: G 19 MET cc_start: 0.6030 (ptt) cc_final: 0.5827 (ptm) REVERT: H 91 MET cc_start: 0.7256 (mpp) cc_final: 0.7028 (mpp) REVERT: I 83 LEU cc_start: 0.3198 (OUTLIER) cc_final: 0.2879 (tt) REVERT: J 58 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4953 (tm-30) REVERT: N 66 PHE cc_start: 0.4201 (OUTLIER) cc_final: 0.3385 (t80) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.1303 time to fit residues: 36.4059 Evaluate side-chains 184 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 289 ILE Chi-restraints excluded: chain T residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 HIS F 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.159717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132509 restraints weight = 32620.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128263 restraints weight = 42698.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129120 restraints weight = 38325.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129774 restraints weight = 27562.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130018 restraints weight = 26748.269| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17989 Z= 0.132 Angle : 0.548 9.626 24301 Z= 0.278 Chirality : 0.038 0.170 2794 Planarity : 0.004 0.049 3119 Dihedral : 4.074 17.149 2380 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.43 % Allowed : 15.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 aren not related in a simple way. whole: 0.74 (0.18), residues: 2210 helix: 1.40 (0.15), residues: 1239 sheet: 0.67 (0.31), residues: 297 loop : -1.29 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 127 TYR 0.012 0.001 TYR B 103 PHE 0.024 0.002 PHE B 82 TRP 0.021 0.001 TRP N 59 HIS 0.003 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00306 (17989) covalent geometry : angle 0.54770 (24301) hydrogen bonds : bond 0.03688 ( 1027) hydrogen bonds : angle 4.27770 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.94 seconds wall clock time: 41 minutes 15.34 seconds (2475.34 seconds total)