Starting phenix.real_space_refine on Sun Jun 15 15:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2u_28827/06_2025/8f2u_28827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2u_28827/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f2u_28827/06_2025/8f2u_28827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2u_28827/06_2025/8f2u_28827.map" model { file = "/net/cci-nas-00/data/ceres_data/8f2u_28827/06_2025/8f2u_28827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2u_28827/06_2025/8f2u_28827.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.77, per 1000 atoms: 0.61 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: 4.91 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.92 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: 5.30 Time building geometry restraints manager: 5.79 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: 1.180 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.820 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (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 TRP 0.012 0.001 TRP N 59 HIS 0.005 0.001 HIS J 69 PHE 0.014 0.001 PHE G 38 TYR 0.017 0.001 TYR B 67 ARG 0.009 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.17572 ( 1027) hydrogen bonds : angle 6.60588 ( 3009) covalent geometry : bond 0.00245 (17989) covalent geometry : angle 0.56030 (24301) *********************** 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 : 1.991 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: 0.3000 time to fit residues: 104.4745 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 : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** C 76 HIS C 106 ASN D 102 HIS D 118 GLN D 190 GLN E 95 GLN F 52 HIS ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN N 82 GLN N 147 GLN T 246 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.161219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.136739 restraints weight = 33064.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135586 restraints weight = 57796.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136617 restraints weight = 59968.874| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17989 Z= 0.202 Angle : 0.655 8.448 24301 Z= 0.335 Chirality : 0.043 0.204 2794 Planarity : 0.005 0.060 3119 Dihedral : 4.351 17.854 2380 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.02 % Allowed : 8.87 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2210 helix: 1.24 (0.15), residues: 1225 sheet: 0.48 (0.31), residues: 290 loop : -1.39 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 123 HIS 0.011 0.001 HIS J 42 PHE 0.027 0.002 PHE D 5 TYR 0.017 0.002 TYR B 67 ARG 0.007 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 1027) hydrogen bonds : angle 5.00210 ( 3009) covalent geometry : bond 0.00465 (17989) covalent geometry : angle 0.65502 (24301) *********************** 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 192 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 2.188 Fit side-chains REVERT: A 110 MET cc_start: 0.6209 (mtm) cc_final: 0.6002 (mtp) REVERT: E 115 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4246 (pm20) REVERT: F 48 LYS cc_start: 0.7582 (ptmt) cc_final: 0.7113 (mtpt) REVERT: H 91 MET cc_start: 0.6800 (mpp) cc_final: 0.6517 (mpp) REVERT: H 119 ASP cc_start: 0.7650 (p0) cc_final: 0.7325 (p0) REVERT: J 75 ILE cc_start: 0.7665 (mm) cc_final: 0.7338 (mt) REVERT: N 66 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.3035 (t80) REVERT: N 287 LYS cc_start: 0.4066 (ttmt) cc_final: 0.3548 (tppt) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.2980 time to fit residues: 83.9777 Evaluate side-chains 168 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 19 ILE Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 120 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 178 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 29 optimal weight: 0.0170 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN J 86 ASN N 121 GLN T 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.131337 restraints weight = 32384.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130144 restraints weight = 53863.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131376 restraints weight = 48616.217| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17989 Z= 0.182 Angle : 0.606 9.017 24301 Z= 0.310 Chirality : 0.040 0.171 2794 Planarity : 0.005 0.050 3119 Dihedral : 4.344 18.104 2380 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.48 % Allowed : 11.72 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2210 helix: 1.15 (0.15), residues: 1216 sheet: 0.35 (0.30), residues: 297 loop : -1.39 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 98 HIS 0.009 0.001 HIS J 42 PHE 0.023 0.002 PHE J 30 TYR 0.012 0.002 TYR C 86 ARG 0.005 0.000 ARG J 127 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 1027) hydrogen bonds : angle 4.80988 ( 3009) covalent geometry : bond 0.00426 (17989) covalent geometry : angle 0.60624 (24301) *********************** 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 197 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 2.096 Fit side-chains REVERT: B 15 PHE cc_start: 0.6259 (t80) cc_final: 0.5949 (t80) REVERT: E 115 GLU cc_start: 0.5667 (mm-30) cc_final: 0.4373 (pm20) REVERT: F 48 LYS cc_start: 0.7607 (ptmt) cc_final: 0.7109 (mtpt) REVERT: G 1 MET cc_start: 0.3330 (OUTLIER) cc_final: 0.2703 (ttm) REVERT: H 91 MET cc_start: 0.7114 (mpp) cc_final: 0.6795 (mpp) REVERT: H 119 ASP cc_start: 0.7867 (p0) cc_final: 0.7659 (p0) REVERT: I 83 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2337 (tt) REVERT: J 75 ILE cc_start: 0.7975 (mm) cc_final: 0.7631 (mt) REVERT: N 66 PHE cc_start: 0.4094 (OUTLIER) cc_final: 0.3143 (t80) REVERT: N 287 LYS cc_start: 0.3515 (ttmt) cc_final: 0.3120 (tppt) outliers start: 29 outliers final: 15 residues processed: 188 average time/residue: 0.2941 time to fit residues: 85.0535 Evaluate side-chains 170 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE 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 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 G residue 1 MET Chi-restraints excluded: chain G residue 192 VAL 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 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 13 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 17 optimal weight: 0.0370 chunk 77 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 overall best weight: 1.7660 ------------------------------------------------------------------------------- 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 118 GLN F 52 HIS G 80 ASN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.162158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136621 restraints weight = 32138.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136280 restraints weight = 56736.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.137119 restraints weight = 53116.312| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17989 Z= 0.118 Angle : 0.527 9.113 24301 Z= 0.269 Chirality : 0.038 0.146 2794 Planarity : 0.004 0.050 3119 Dihedral : 4.079 17.723 2380 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.48 % Allowed : 12.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2210 helix: 1.39 (0.15), residues: 1226 sheet: 0.51 (0.30), residues: 290 loop : -1.31 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.008 0.001 HIS J 42 PHE 0.021 0.001 PHE D 5 TYR 0.012 0.001 TYR N 176 ARG 0.009 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1027) hydrogen bonds : angle 4.44925 ( 3009) covalent geometry : bond 0.00261 (17989) covalent geometry : angle 0.52666 (24301) *********************** 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 : 2.473 Fit side-chains REVERT: E 115 GLU cc_start: 0.5748 (mm-30) cc_final: 0.4424 (pm20) REVERT: F 48 LYS cc_start: 0.7480 (ptmt) cc_final: 0.7009 (mtpt) REVERT: G 1 MET cc_start: 0.3400 (OUTLIER) cc_final: 0.2771 (ttm) REVERT: G 123 TRP cc_start: 0.6588 (t60) cc_final: 0.6384 (t60) REVERT: H 91 MET cc_start: 0.7095 (mpp) cc_final: 0.6785 (mpp) REVERT: J 75 ILE cc_start: 0.8002 (mm) cc_final: 0.7649 (mt) REVERT: N 66 PHE cc_start: 0.4023 (OUTLIER) cc_final: 0.2931 (t80) REVERT: N 160 LYS cc_start: 0.7173 (mtmm) cc_final: 0.6261 (tptp) outliers start: 29 outliers final: 17 residues processed: 190 average time/residue: 0.3446 time to fit residues: 100.3335 Evaluate side-chains 177 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 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 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 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 123 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS C 106 ASN F 52 HIS I 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.157586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131818 restraints weight = 32829.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132926 restraints weight = 60706.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133368 restraints weight = 42317.810| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3003 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= 0.208 Angle : 0.643 9.640 24301 Z= 0.328 Chirality : 0.041 0.160 2794 Planarity : 0.005 0.052 3119 Dihedral : 4.491 17.680 2380 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.09 % Allowed : 13.91 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2210 helix: 1.01 (0.15), residues: 1222 sheet: 0.25 (0.30), residues: 297 loop : -1.49 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 59 HIS 0.007 0.001 HIS A 101 PHE 0.019 0.002 PHE J 30 TYR 0.015 0.002 TYR N 205 ARG 0.005 0.001 ARG T 245 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1027) hydrogen bonds : angle 4.75450 ( 3009) covalent geometry : bond 0.00494 (17989) covalent geometry : angle 0.64340 (24301) *********************** 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 207 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 2.042 Fit side-chains REVERT: B 15 PHE cc_start: 0.6226 (t80) cc_final: 0.5832 (t80) REVERT: C 172 MET cc_start: 0.7117 (ttt) cc_final: 0.6731 (ttt) REVERT: E 115 GLU cc_start: 0.5685 (mm-30) cc_final: 0.4348 (pm20) REVERT: E 208 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8575 (mm) REVERT: F 48 LYS cc_start: 0.7602 (ptmt) cc_final: 0.7113 (mtpt) REVERT: G 1 MET cc_start: 0.3426 (OUTLIER) cc_final: 0.2861 (ttm) REVERT: H 91 MET cc_start: 0.7288 (mpp) cc_final: 0.7011 (mpp) REVERT: I 83 LEU cc_start: 0.2845 (OUTLIER) cc_final: 0.2405 (tt) REVERT: J 75 ILE cc_start: 0.8162 (mm) cc_final: 0.7777 (mt) REVERT: N 66 PHE cc_start: 0.4253 (OUTLIER) cc_final: 0.3363 (t80) outliers start: 41 outliers final: 28 residues processed: 196 average time/residue: 0.2777 time to fit residues: 85.2381 Evaluate side-chains 182 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 195 VAL 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 D residue 154 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 VAL 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 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 120 VAL Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 I 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135277 restraints weight = 32884.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135861 restraints weight = 63025.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136177 restraints weight = 48407.977| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17989 Z= 0.151 Angle : 0.560 9.652 24301 Z= 0.286 Chirality : 0.039 0.145 2794 Planarity : 0.004 0.052 3119 Dihedral : 4.301 16.870 2380 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.24 % Allowed : 14.83 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2210 helix: 1.20 (0.15), residues: 1226 sheet: 0.31 (0.30), residues: 297 loop : -1.44 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 59 HIS 0.004 0.001 HIS D 156 PHE 0.017 0.002 PHE D 5 TYR 0.011 0.001 TYR C 86 ARG 0.003 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 1027) hydrogen bonds : angle 4.51494 ( 3009) covalent geometry : bond 0.00349 (17989) covalent geometry : angle 0.55971 (24301) *********************** 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 208 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 3.184 Fit side-chains REVERT: D 51 ILE cc_start: 0.8221 (pt) cc_final: 0.7940 (pt) REVERT: E 115 GLU cc_start: 0.5695 (mm-30) cc_final: 0.4424 (pm20) REVERT: E 208 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8550 (mm) REVERT: F 48 LYS cc_start: 0.7453 (ptmt) cc_final: 0.6985 (mtpt) REVERT: G 1 MET cc_start: 0.3656 (OUTLIER) cc_final: 0.3080 (ttm) REVERT: H 91 MET cc_start: 0.7262 (mpp) cc_final: 0.6994 (mpp) REVERT: H 119 ASP cc_start: 0.7935 (p0) cc_final: 0.7665 (p0) REVERT: I 83 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2218 (tt) REVERT: J 75 ILE cc_start: 0.8080 (mm) cc_final: 0.7730 (mt) REVERT: N 66 PHE cc_start: 0.4321 (OUTLIER) cc_final: 0.3384 (t80) outliers start: 44 outliers final: 28 residues processed: 198 average time/residue: 0.3118 time to fit residues: 96.1729 Evaluate side-chains 191 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 43 ILE 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 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 99 LEU 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 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 65 HIS 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 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 120 VAL Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.158173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133170 restraints weight = 32554.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132468 restraints weight = 65559.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133485 restraints weight = 53080.178| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17989 Z= 0.169 Angle : 0.584 9.758 24301 Z= 0.298 Chirality : 0.040 0.149 2794 Planarity : 0.004 0.052 3119 Dihedral : 4.328 16.523 2380 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.50 % Allowed : 15.14 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2210 helix: 1.17 (0.15), residues: 1222 sheet: 0.23 (0.30), residues: 298 loop : -1.47 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 59 HIS 0.004 0.001 HIS A 101 PHE 0.017 0.002 PHE J 30 TYR 0.011 0.002 TYR D 48 ARG 0.002 0.000 ARG D 158 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1027) hydrogen bonds : angle 4.54121 ( 3009) covalent geometry : bond 0.00397 (17989) covalent geometry : angle 0.58405 (24301) *********************** 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 214 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 3.438 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: D 51 ILE cc_start: 0.8205 (pt) cc_final: 0.7933 (pt) REVERT: E 115 GLU cc_start: 0.5679 (mm-30) cc_final: 0.4997 (tt0) REVERT: E 208 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8558 (mm) REVERT: F 48 LYS cc_start: 0.7470 (ptmt) cc_final: 0.7017 (mtpt) REVERT: G 1 MET cc_start: 0.3596 (OUTLIER) cc_final: 0.3386 (ttp) REVERT: H 91 MET cc_start: 0.7268 (mpp) cc_final: 0.7021 (mpp) REVERT: I 83 LEU cc_start: 0.2973 (OUTLIER) cc_final: 0.2595 (tt) REVERT: J 75 ILE cc_start: 0.8138 (mm) cc_final: 0.7769 (mt) REVERT: N 66 PHE cc_start: 0.4314 (OUTLIER) cc_final: 0.3381 (t80) REVERT: N 147 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.6216 (mm-40) outliers start: 49 outliers final: 35 residues processed: 203 average time/residue: 0.2867 time to fit residues: 91.5722 Evaluate side-chains 204 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 112 THR 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 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 99 LEU 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 G residue 1 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 65 HIS 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 37 ILE Chi-restraints excluded: chain J residue 177 VAL 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 120 VAL Chi-restraints excluded: chain N residue 147 GLN Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 24 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 184 optimal weight: 0.0970 chunk 4 optimal weight: 0.4980 chunk 142 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 chunk 86 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135078 restraints weight = 32456.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134366 restraints weight = 56803.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135374 restraints weight = 49454.083| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17989 Z= 0.101 Angle : 0.504 9.536 24301 Z= 0.257 Chirality : 0.037 0.131 2794 Planarity : 0.004 0.052 3119 Dihedral : 3.924 17.741 2380 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 16.72 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2210 helix: 1.56 (0.15), residues: 1232 sheet: 0.61 (0.31), residues: 287 loop : -1.18 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 59 HIS 0.004 0.001 HIS J 147 PHE 0.019 0.001 PHE D 5 TYR 0.010 0.001 TYR C 86 ARG 0.003 0.000 ARG J 127 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1027) hydrogen bonds : angle 4.19866 ( 3009) covalent geometry : bond 0.00218 (17989) covalent geometry : angle 0.50398 (24301) *********************** 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 206 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 2.068 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: D 51 ILE cc_start: 0.8045 (pt) cc_final: 0.7774 (pt) REVERT: E 115 GLU cc_start: 0.5672 (mm-30) cc_final: 0.4915 (tt0) REVERT: F 48 LYS cc_start: 0.7348 (ptmt) cc_final: 0.7008 (mtpt) REVERT: G 1 MET cc_start: 0.3691 (OUTLIER) cc_final: 0.3110 (ttm) REVERT: H 91 MET cc_start: 0.7250 (mpp) cc_final: 0.7039 (mpp) REVERT: H 119 ASP cc_start: 0.7758 (p0) cc_final: 0.7363 (p0) REVERT: J 75 ILE cc_start: 0.8131 (mm) cc_final: 0.7765 (mt) REVERT: N 66 PHE cc_start: 0.4164 (OUTLIER) cc_final: 0.3349 (t80) REVERT: N 111 MET cc_start: 0.1453 (mmm) cc_final: 0.1043 (mmm) outliers start: 29 outliers final: 19 residues processed: 200 average time/residue: 0.2715 time to fit residues: 85.0049 Evaluate side-chains 186 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU 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 16 LEU 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 F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 139 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 206 optimal weight: 0.0670 chunk 91 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- 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 N 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.160458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134757 restraints weight = 32682.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134042 restraints weight = 55494.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135090 restraints weight = 48379.152| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17989 Z= 0.110 Angle : 0.519 9.545 24301 Z= 0.262 Chirality : 0.037 0.147 2794 Planarity : 0.004 0.051 3119 Dihedral : 3.878 17.148 2380 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.33 % Allowed : 17.02 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2210 helix: 1.59 (0.15), residues: 1233 sheet: 0.66 (0.31), residues: 288 loop : -1.15 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 59 HIS 0.003 0.001 HIS J 42 PHE 0.018 0.001 PHE N 146 TYR 0.011 0.001 TYR C 86 ARG 0.006 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1027) hydrogen bonds : angle 4.15488 ( 3009) covalent geometry : bond 0.00245 (17989) covalent geometry : angle 0.51905 (24301) *********************** 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 194 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: D 51 ILE cc_start: 0.8031 (pt) cc_final: 0.7773 (pt) REVERT: E 115 GLU cc_start: 0.5550 (mm-30) cc_final: 0.4856 (tt0) REVERT: E 178 MET cc_start: 0.8500 (mtm) cc_final: 0.8261 (mtm) REVERT: F 48 LYS cc_start: 0.7352 (ptmt) cc_final: 0.7030 (mtpt) REVERT: G 1 MET cc_start: 0.3715 (OUTLIER) cc_final: 0.3156 (ttm) REVERT: H 91 MET cc_start: 0.7246 (mpp) cc_final: 0.7037 (mpp) REVERT: H 119 ASP cc_start: 0.7626 (p0) cc_final: 0.7243 (p0) REVERT: I 83 LEU cc_start: 0.3204 (OUTLIER) cc_final: 0.2880 (tt) REVERT: J 75 ILE cc_start: 0.8133 (mm) cc_final: 0.7759 (mt) REVERT: N 66 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.3458 (t80) REVERT: N 111 MET cc_start: 0.1621 (mmm) cc_final: 0.1187 (mmm) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.2858 time to fit residues: 83.8866 Evaluate side-chains 183 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU 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 16 LEU 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 F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 65 HIS Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 162 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 185 optimal weight: 0.0010 chunk 151 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 T 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.161410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133978 restraints weight = 32496.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132069 restraints weight = 49929.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133231 restraints weight = 46291.629| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17989 Z= 0.100 Angle : 0.513 9.612 24301 Z= 0.258 Chirality : 0.037 0.143 2794 Planarity : 0.004 0.051 3119 Dihedral : 3.771 17.629 2380 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.38 % Allowed : 17.07 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2210 helix: 1.69 (0.15), residues: 1232 sheet: 0.78 (0.31), residues: 288 loop : -1.11 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 59 HIS 0.003 0.001 HIS J 147 PHE 0.019 0.001 PHE N 146 TYR 0.011 0.001 TYR C 86 ARG 0.008 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 1027) hydrogen bonds : angle 4.06658 ( 3009) covalent geometry : bond 0.00219 (17989) covalent geometry : angle 0.51264 (24301) ********************** 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 200 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 2.708 Fit side-chains revert: symmetry clash REVERT: D 51 ILE cc_start: 0.7932 (pt) cc_final: 0.7662 (pt) REVERT: E 115 GLU cc_start: 0.5556 (mm-30) cc_final: 0.4874 (tt0) REVERT: E 178 MET cc_start: 0.8458 (mtm) cc_final: 0.8216 (mtm) REVERT: F 48 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6978 (mtpt) REVERT: G 1 MET cc_start: 0.3544 (OUTLIER) cc_final: 0.3030 (ttm) REVERT: H 91 MET cc_start: 0.7155 (mpp) cc_final: 0.6948 (mpp) REVERT: H 119 ASP cc_start: 0.7566 (p0) cc_final: 0.7282 (p0) REVERT: I 83 LEU cc_start: 0.3383 (OUTLIER) cc_final: 0.3068 (tt) REVERT: J 75 ILE cc_start: 0.8087 (mm) cc_final: 0.7639 (mt) REVERT: N 57 MET cc_start: 0.4612 (mmt) cc_final: 0.3669 (mtm) REVERT: N 66 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3483 (t80) REVERT: N 111 MET cc_start: 0.1571 (mmm) cc_final: 0.1197 (mmm) REVERT: N 136 ASP cc_start: 0.3276 (p0) cc_final: 0.2958 (p0) REVERT: N 292 GLU cc_start: 0.3602 (tp30) cc_final: 0.2566 (pt0) outliers start: 27 outliers final: 21 residues processed: 194 average time/residue: 0.4413 time to fit residues: 131.9332 Evaluate side-chains 190 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 3.128 ------------------------------------------------------------------------------- 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 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 65 HIS Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 162 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 0.0020 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 19 optimal weight: 0.0170 chunk 209 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 overall best weight: 2.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 HIS I 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.159095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.132720 restraints weight = 32595.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.133376 restraints weight = 55281.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134266 restraints weight = 41937.257| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17989 Z= 0.146 Angle : 0.566 9.692 24301 Z= 0.286 Chirality : 0.039 0.140 2794 Planarity : 0.004 0.051 3119 Dihedral : 3.987 16.291 2380 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.48 % Allowed : 17.28 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2210 helix: 1.49 (0.15), residues: 1238 sheet: 0.57 (0.31), residues: 297 loop : -1.22 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 59 HIS 0.004 0.001 HIS A 101 PHE 0.019 0.002 PHE N 146 TYR 0.012 0.001 TYR D 48 ARG 0.004 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1027) hydrogen bonds : angle 4.25359 ( 3009) covalent geometry : bond 0.00340 (17989) covalent geometry : angle 0.56585 (24301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5671.35 seconds wall clock time: 102 minutes 37.17 seconds (6157.17 seconds total)