Starting phenix.real_space_refine on Tue Jun 24 22:30:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.map" model { file = "/net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2r_28825/06_2025/8f2r_28825.cif" } resolution = 3.12 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= 0.029 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 9189 2.51 5 N 2499 2.21 5 O 2748 1.98 5 H 14772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29276 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2940 Classifications: {'peptide': 187} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3240 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3095 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "D" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3093 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "E" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3239 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1239 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3186 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "H" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2928 Classifications: {'peptide': 179} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "I" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3104 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "J" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3212 Classifications: {'peptide': 198} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Time building chain proxies: 13.34, per 1000 atoms: 0.46 Number of scatterers: 29276 At special positions: 0 Unit cell: (121.408, 132.248, 132.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 2748 8.00 N 2499 7.00 C 9189 6.00 H 14772 1.00 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: 7.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3524 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 5 sheets defined 64.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.805A pdb=" N LEU A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 44 through 64 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 87 through 113 removed outlier: 7.412A pdb=" N THR A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 20 through 38 removed outlier: 4.400A pdb=" N ARG B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.997A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 76 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 106 through 115 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 188 removed outlier: 3.933A pdb=" N MET B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 93 through 117 removed outlier: 5.040A pdb=" N ASN C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 4.209A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 12 through 24 removed outlier: 4.230A pdb=" N SER D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 61 through 83 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.606A pdb=" N CYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Proline residue: D 116 - end of helix Processing helix chain 'D' and resid 178 through 199 removed outlier: 3.635A pdb=" N SER D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 78 through 99 removed outlier: 3.726A pdb=" N LEU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.065A pdb=" N LEU E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 4.257A pdb=" N ALA E 147 " --> pdb=" O GLN E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 193 through 222 removed outlier: 3.638A pdb=" N ARG E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 4.105A pdb=" N VAL F 15 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.732A pdb=" N GLY G 16 " --> pdb=" O PRO G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 Processing helix chain 'G' and resid 46 through 62 Processing helix chain 'G' and resid 64 through 86 removed outlier: 4.831A pdb=" N VAL G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 179 through 198 Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.581A pdb=" N ARG H 11 " --> pdb=" O PRO H 8 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 14 " --> pdb=" O ARG H 11 " (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 32 removed outlier: 3.516A pdb=" N LEU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.918A pdb=" N ALA H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 83 through 96 Processing helix chain 'H' and resid 97 through 111 removed outlier: 3.749A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 183 removed outlier: 3.702A pdb=" N VAL H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 14 through 18 Processing helix chain 'I' and resid 20 through 34 removed outlier: 3.706A pdb=" N VAL I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 4.157A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'I' and resid 91 through 117 removed outlier: 4.004A pdb=" N LEU I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 Processing helix chain 'I' and resid 174 through 198 removed outlier: 4.622A pdb=" N ARG I 187 " --> pdb=" O ASP I 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE I 188 " --> pdb=" O GLY I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.514A pdb=" N LEU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 64 through 85 Processing helix chain 'J' and resid 88 through 100 Processing helix chain 'J' and resid 102 through 126 removed outlier: 5.911A pdb=" N GLN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 201 Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.576A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TRP A 124 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER I 136 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 126 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 130 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL I 130 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 132 " --> pdb=" O TRP I 128 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP I 128 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU I 123 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN I 154 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP I 125 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL I 144 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 167 removed outlier: 5.704A pdb=" N ASN B 155 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 124 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP B 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER H 130 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 131 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER B 137 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP H 122 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP H 146 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE H 120 " --> pdb=" O HIS H 144 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS H 144 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP H 122 " --> pdb=" O SER H 142 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER H 142 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL H 124 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU H 140 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU H 126 " --> pdb=" O MET H 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET H 138 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 165 through 170 removed outlier: 6.143A pdb=" N GLN C 156 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 125 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP C 130 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS J 147 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 132 " --> pdb=" O MET J 145 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU J 141 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR C 138 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP J 139 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY J 163 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL J 137 " --> pdb=" O GLN J 161 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN J 161 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP J 139 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 159 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU J 141 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN J 157 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 158 " --> pdb=" O PHE J 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 177 removed outlier: 3.650A pdb=" N GLY D 133 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 162 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU D 131 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP D 136 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER F 32 " --> pdb=" O TRP D 136 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 138 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU F 26 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER D 144 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TRP F 24 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU F 19 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 50 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.741A pdb=" N SER E 175 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL E 159 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 177 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 157 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN E 179 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE E 155 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 181 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP E 157 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER G 147 " --> pdb=" O TRP E 157 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 159 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU G 134 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS G 165 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP G 136 " --> pdb=" O VAL G 163 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2844 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: 9.83 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14745 1.03 - 1.22: 28 1.22 - 1.42: 5937 1.42 - 1.62: 8696 1.62 - 1.81: 109 Bond restraints: 29515 Sorted by residual: bond pdb=" CB PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 bond pdb=" CG GLN I 114 " pdb=" CD GLN I 114 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" N LEU E 149 " pdb=" CA LEU E 149 " ideal model delta sigma weight residual 1.454 1.474 -0.021 1.74e-02 3.30e+03 1.44e+00 bond pdb=" CG PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.33e+00 bond pdb=" CB ASP F 51 " pdb=" CG ASP F 51 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 ... (remaining 29510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 49253 1.28 - 2.55: 3953 2.55 - 3.83: 286 3.83 - 5.10: 55 5.10 - 6.38: 16 Bond angle restraints: 53563 Sorted by residual: angle pdb=" CA PRO H 71 " pdb=" N PRO H 71 " pdb=" CD PRO H 71 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 angle pdb=" N PRO H 71 " pdb=" CD PRO H 71 " pdb=" CG PRO H 71 " ideal model delta sigma weight residual 103.20 98.30 4.90 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N ASN C 109 " pdb=" CA ASN C 109 " pdb=" C ASN C 109 " ideal model delta sigma weight residual 111.82 115.57 -3.75 1.16e+00 7.43e-01 1.05e+01 angle pdb=" CA TYR F 40 " pdb=" CB TYR F 40 " pdb=" CG TYR F 40 " ideal model delta sigma weight residual 113.90 119.56 -5.66 1.80e+00 3.09e-01 9.87e+00 angle pdb=" N MET D 128 " pdb=" CA MET D 128 " pdb=" C MET D 128 " ideal model delta sigma weight residual 109.39 114.18 -4.79 1.59e+00 3.96e-01 9.08e+00 ... (remaining 53558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12404 17.81 - 35.62: 838 35.62 - 53.42: 257 53.42 - 71.23: 205 71.23 - 89.04: 24 Dihedral angle restraints: 13728 sinusoidal: 7618 harmonic: 6110 Sorted by residual: dihedral pdb=" CA CYS C 170 " pdb=" C CYS C 170 " pdb=" N SER C 171 " pdb=" CA SER C 171 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASP E 63 " pdb=" C ASP E 63 " pdb=" N CYS E 64 " pdb=" CA CYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N HIS A 139 " pdb=" CA HIS A 139 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 13725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1714 0.043 - 0.087: 455 0.087 - 0.130: 112 0.130 - 0.174: 25 0.174 - 0.217: 3 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA ARG B 141 " pdb=" N ARG B 141 " pdb=" C ARG B 141 " pdb=" CB ARG B 141 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR C 145 " pdb=" N TYR C 145 " pdb=" C TYR C 145 " pdb=" CB TYR C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2306 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 170 " -0.203 9.50e-02 1.11e+02 7.87e-02 4.08e+01 pdb=" NE ARG E 170 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG E 170 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG E 170 " 0.084 2.00e-02 2.50e+03 pdb=" NH2 ARG E 170 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG E 170 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG E 170 " -0.079 2.00e-02 2.50e+03 pdb="HH21 ARG E 170 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 170 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 110 " -0.122 9.50e-02 1.11e+02 5.79e-02 3.98e+01 pdb=" NE ARG I 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG I 110 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 110 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG I 110 " 0.071 2.00e-02 2.50e+03 pdb="HH11 ARG I 110 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG I 110 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG I 110 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG I 110 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " 0.144 9.50e-02 1.11e+02 6.17e-02 3.65e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.075 2.00e-02 2.50e+03 pdb="HH11 ARG A 125 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 125 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 125 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 125 " 0.076 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 750 2.12 - 2.74: 53464 2.74 - 3.36: 83524 3.36 - 3.98: 102357 3.98 - 4.60: 163404 Nonbonded interactions: 403499 Sorted by model distance: nonbonded pdb=" HH TYR D 140 " pdb=" OE1 GLU D 151 " model vdw 1.504 2.450 nonbonded pdb=" OE1 GLU A 162 " pdb=" HG1 THR F 16 " model vdw 1.510 2.450 nonbonded pdb=" OE1 GLU H 49 " pdb=" H GLU H 49 " model vdw 1.515 2.450 nonbonded pdb=" OE1 GLN E 120 " pdb=" H GLN E 120 " model vdw 1.520 2.450 nonbonded pdb=" OE1 GLN F 18 " pdb=" H GLN F 18 " model vdw 1.565 2.450 ... (remaining 403494 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 individual isotropic 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: 3.310 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: 0.470 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 56.430 Find NCS groups from input model: 0.450 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.004 0.068 14743 Z= 0.192 Angle : 0.797 6.379 19911 Z= 0.482 Chirality : 0.043 0.217 2309 Planarity : 0.010 0.123 2547 Dihedral : 15.266 89.040 5566 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.20 % Favored : 97.63 % Rotamer: Outliers : 0.12 % Allowed : 11.27 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.18), residues: 1817 helix: 0.07 (0.14), residues: 1093 sheet: 0.77 (0.28), residues: 287 loop : -0.03 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP E 148 HIS 0.009 0.002 HIS J 181 PHE 0.021 0.003 PHE G 96 TYR 0.031 0.005 TYR C 134 ARG 0.024 0.003 ARG D 127 Details of bonding type rmsd hydrogen bonds : bond 0.13029 ( 981) hydrogen bonds : angle 6.19719 ( 2844) covalent geometry : bond 0.00398 (14743) covalent geometry : angle 0.79653 (19911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 MET cc_start: 0.6232 (mmm) cc_final: 0.5845 (mmm) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.8586 time to fit residues: 229.5640 Evaluate side-chains 157 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN E 94 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.219302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155478 restraints weight = 53433.566| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.48 r_work: 0.3697 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14743 Z= 0.151 Angle : 0.578 5.217 19911 Z= 0.313 Chirality : 0.038 0.188 2309 Planarity : 0.005 0.068 2547 Dihedral : 4.737 20.954 1945 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.68 % Rotamer: Outliers : 1.05 % Allowed : 10.53 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.19), residues: 1817 helix: 1.50 (0.15), residues: 1099 sheet: 0.50 (0.28), residues: 297 loop : 0.57 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 14 HIS 0.006 0.001 HIS J 147 PHE 0.015 0.002 PHE C 11 TYR 0.019 0.001 TYR F 40 ARG 0.004 0.001 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 981) hydrogen bonds : angle 4.88595 ( 2844) covalent geometry : bond 0.00324 (14743) covalent geometry : angle 0.57770 (19911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7410 (mtp) cc_final: 0.7205 (mtp) REVERT: E 36 MET cc_start: 0.8301 (ttp) cc_final: 0.8038 (tmm) REVERT: E 65 ARG cc_start: 0.5645 (mtm-85) cc_final: 0.4169 (mmt-90) REVERT: I 92 GLN cc_start: 0.5601 (mp10) cc_final: 0.5202 (mm-40) REVERT: J 44 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7279 (tppt) REVERT: J 144 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8214 (tp40) outliers start: 17 outliers final: 12 residues processed: 182 average time/residue: 0.7039 time to fit residues: 176.8551 Evaluate side-chains 161 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 156 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.213196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147013 restraints weight = 51634.617| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.47 r_work: 0.3637 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14743 Z= 0.154 Angle : 0.534 5.071 19911 Z= 0.286 Chirality : 0.037 0.165 2309 Planarity : 0.004 0.052 2547 Dihedral : 4.390 26.570 1945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Rotamer: Outliers : 1.80 % Allowed : 10.34 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.20), residues: 1817 helix: 1.85 (0.15), residues: 1103 sheet: 0.39 (0.27), residues: 291 loop : 0.23 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 46 HIS 0.008 0.002 HIS J 42 PHE 0.017 0.002 PHE G 141 TYR 0.020 0.002 TYR F 40 ARG 0.005 0.001 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 981) hydrogen bonds : angle 4.51886 ( 2844) covalent geometry : bond 0.00353 (14743) covalent geometry : angle 0.53421 (19911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.6152 (mtm-85) cc_final: 0.4081 (mmt-90) REVERT: E 81 GLN cc_start: 0.6888 (mt0) cc_final: 0.6600 (tt0) REVERT: F 18 GLN cc_start: 0.7079 (pm20) cc_final: 0.6184 (mm-40) REVERT: G 148 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8892 (p) REVERT: H 34 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7579 (mtm-85) REVERT: H 53 HIS cc_start: 0.7068 (m-70) cc_final: 0.6666 (m-70) REVERT: H 154 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7893 (mmtm) REVERT: I 29 GLN cc_start: 0.7570 (mt0) cc_final: 0.7151 (tm-30) REVERT: I 91 HIS cc_start: 0.7558 (m90) cc_final: 0.7347 (m-70) REVERT: I 92 GLN cc_start: 0.5306 (mp10) cc_final: 0.5002 (mm110) REVERT: J 44 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7104 (tppt) outliers start: 29 outliers final: 19 residues processed: 176 average time/residue: 0.7472 time to fit residues: 182.9525 Evaluate side-chains 167 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 152 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS J 126 GLN J 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.213096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144258 restraints weight = 53186.733| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.48 r_work: 0.3618 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14743 Z= 0.138 Angle : 0.510 4.937 19911 Z= 0.271 Chirality : 0.036 0.164 2309 Planarity : 0.004 0.044 2547 Dihedral : 4.189 28.259 1945 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 1.55 % Allowed : 10.84 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.20), residues: 1817 helix: 2.05 (0.15), residues: 1102 sheet: 0.28 (0.27), residues: 291 loop : 0.09 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 46 HIS 0.008 0.001 HIS J 147 PHE 0.016 0.001 PHE G 141 TYR 0.018 0.001 TYR F 40 ARG 0.003 0.000 ARG J 36 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 981) hydrogen bonds : angle 4.36920 ( 2844) covalent geometry : bond 0.00316 (14743) covalent geometry : angle 0.51000 (19911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.4818 (mtm-85) cc_final: 0.4559 (ttp80) REVERT: C 99 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7040 (tp) REVERT: E 65 ARG cc_start: 0.6178 (mtm-85) cc_final: 0.4103 (mmt180) REVERT: E 81 GLN cc_start: 0.6812 (mt0) cc_final: 0.6507 (tt0) REVERT: F 18 GLN cc_start: 0.7060 (pm20) cc_final: 0.6298 (mm-40) REVERT: G 148 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8914 (p) REVERT: H 34 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7455 (mtm-85) REVERT: H 154 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7996 (mmtp) REVERT: I 29 GLN cc_start: 0.7552 (mt0) cc_final: 0.7126 (tm-30) REVERT: I 91 HIS cc_start: 0.7533 (m90) cc_final: 0.7256 (m-70) REVERT: I 92 GLN cc_start: 0.5403 (mp10) cc_final: 0.5124 (mm110) REVERT: J 44 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7088 (tppt) outliers start: 25 outliers final: 19 residues processed: 178 average time/residue: 0.7308 time to fit residues: 180.9164 Evaluate side-chains 172 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 87 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.210904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144030 restraints weight = 51487.785| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.48 r_work: 0.3598 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14743 Z= 0.133 Angle : 0.494 4.749 19911 Z= 0.264 Chirality : 0.036 0.171 2309 Planarity : 0.004 0.044 2547 Dihedral : 4.076 23.766 1945 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.55 % Allowed : 11.39 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1817 helix: 2.15 (0.16), residues: 1103 sheet: 0.25 (0.27), residues: 291 loop : 0.06 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 PHE 0.014 0.001 PHE G 141 TYR 0.016 0.001 TYR F 40 ARG 0.003 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 981) hydrogen bonds : angle 4.28394 ( 2844) covalent geometry : bond 0.00304 (14743) covalent geometry : angle 0.49444 (19911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.4898 (mtm-85) cc_final: 0.4614 (ttp80) REVERT: C 99 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7108 (tp) REVERT: D 128 MET cc_start: 0.7667 (mmt) cc_final: 0.7463 (mmt) REVERT: E 25 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7373 (mm) REVERT: E 65 ARG cc_start: 0.6164 (mtm-85) cc_final: 0.4117 (mmt180) REVERT: E 81 GLN cc_start: 0.6889 (mt0) cc_final: 0.6564 (tt0) REVERT: F 18 GLN cc_start: 0.7064 (pm20) cc_final: 0.6393 (mm-40) REVERT: G 148 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8940 (p) REVERT: H 34 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7614 (mtm-85) REVERT: H 53 HIS cc_start: 0.6958 (m-70) cc_final: 0.6541 (m-70) REVERT: H 154 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8015 (mmtp) REVERT: I 29 GLN cc_start: 0.7541 (mt0) cc_final: 0.7127 (tm-30) REVERT: J 36 ARG cc_start: 0.7110 (tpp-160) cc_final: 0.6802 (tpt90) REVERT: J 44 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7050 (tppt) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.7048 time to fit residues: 168.9585 Evaluate side-chains 170 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 2 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 ASN J 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.204307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133681 restraints weight = 53119.067| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.62 r_work: 0.3475 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 14743 Z= 0.307 Angle : 0.699 6.679 19911 Z= 0.381 Chirality : 0.043 0.177 2309 Planarity : 0.006 0.056 2547 Dihedral : 4.700 30.587 1945 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 2.17 % Allowed : 11.58 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.19), residues: 1817 helix: 1.38 (0.15), residues: 1105 sheet: -0.24 (0.27), residues: 292 loop : -0.73 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 115 HIS 0.014 0.003 HIS B 153 PHE 0.023 0.003 PHE E 155 TYR 0.031 0.003 TYR F 40 ARG 0.009 0.001 ARG E 158 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 981) hydrogen bonds : angle 4.83166 ( 2844) covalent geometry : bond 0.00733 (14743) covalent geometry : angle 0.69882 (19911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.5072 (mtm-85) cc_final: 0.4857 (ttp80) REVERT: D 2 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7362 (mmt-90) REVERT: D 8 ASP cc_start: 0.8173 (m-30) cc_final: 0.7942 (m-30) REVERT: D 128 MET cc_start: 0.7776 (mmt) cc_final: 0.7451 (mpp) REVERT: E 25 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7733 (mm) REVERT: E 65 ARG cc_start: 0.6590 (mtm-85) cc_final: 0.4525 (mmt180) REVERT: E 81 GLN cc_start: 0.7395 (mt0) cc_final: 0.6984 (tt0) REVERT: E 159 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.7961 (p) REVERT: I 29 GLN cc_start: 0.7574 (mt0) cc_final: 0.7177 (tm-30) REVERT: J 36 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.6874 (tpt90) REVERT: J 44 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7109 (tppt) REVERT: J 165 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7704 (m110) outliers start: 35 outliers final: 25 residues processed: 193 average time/residue: 0.7239 time to fit residues: 195.9876 Evaluate side-chains 169 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 181 GLN E 95 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS H 86 HIS I 191 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.202368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130808 restraints weight = 51723.243| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.52 r_work: 0.3415 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14743 Z= 0.126 Angle : 0.525 5.209 19911 Z= 0.280 Chirality : 0.036 0.153 2309 Planarity : 0.004 0.046 2547 Dihedral : 4.250 27.291 1945 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 12.32 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.20), residues: 1817 helix: 1.91 (0.16), residues: 1104 sheet: -0.18 (0.27), residues: 300 loop : -0.52 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 46 HIS 0.005 0.001 HIS J 181 PHE 0.018 0.001 PHE G 141 TYR 0.017 0.001 TYR F 40 ARG 0.004 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 981) hydrogen bonds : angle 4.40040 ( 2844) covalent geometry : bond 0.00280 (14743) covalent geometry : angle 0.52544 (19911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7594 (tp) REVERT: E 25 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7618 (mm) REVERT: E 65 ARG cc_start: 0.6403 (mtm-85) cc_final: 0.4171 (mmt-90) REVERT: E 81 GLN cc_start: 0.6932 (mt0) cc_final: 0.6552 (tt0) REVERT: I 29 GLN cc_start: 0.7535 (mt0) cc_final: 0.7150 (tm-30) REVERT: J 36 ARG cc_start: 0.7398 (tpp-160) cc_final: 0.6928 (tpt90) REVERT: J 44 LYS cc_start: 0.7736 (mmtt) cc_final: 0.6931 (tppt) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.7304 time to fit residues: 170.8591 Evaluate side-chains 161 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 134 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN H 86 HIS J 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.203258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132295 restraints weight = 52204.183| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.67 r_work: 0.3407 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14743 Z= 0.124 Angle : 0.498 5.021 19911 Z= 0.265 Chirality : 0.035 0.143 2309 Planarity : 0.004 0.045 2547 Dihedral : 3.982 24.682 1945 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 1.49 % Allowed : 12.26 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.20), residues: 1817 helix: 2.23 (0.16), residues: 1104 sheet: -0.15 (0.26), residues: 301 loop : -0.50 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 122 HIS 0.006 0.001 HIS J 147 PHE 0.014 0.001 PHE F 71 TYR 0.011 0.001 TYR F 40 ARG 0.005 0.000 ARG I 25 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 981) hydrogen bonds : angle 4.22969 ( 2844) covalent geometry : bond 0.00281 (14743) covalent geometry : angle 0.49811 (19911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7454 (p0) cc_final: 0.7013 (p0) REVERT: D 1 MET cc_start: 0.6097 (mmt) cc_final: 0.5733 (mmt) REVERT: D 2 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7136 (mmt-90) REVERT: D 8 ASP cc_start: 0.8147 (m-30) cc_final: 0.7875 (m-30) REVERT: E 25 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7584 (mm) REVERT: E 65 ARG cc_start: 0.6390 (mtm-85) cc_final: 0.4289 (mmp-170) REVERT: E 81 GLN cc_start: 0.6907 (mt0) cc_final: 0.6533 (tt0) REVERT: F 35 CYS cc_start: 0.8478 (t) cc_final: 0.8092 (m) REVERT: G 125 ILE cc_start: 0.5314 (OUTLIER) cc_final: 0.5039 (tt) REVERT: H 154 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7867 (mmtp) REVERT: I 29 GLN cc_start: 0.7518 (mt0) cc_final: 0.7113 (tm-30) REVERT: J 36 ARG cc_start: 0.7345 (tpp-160) cc_final: 0.6931 (tpt90) REVERT: J 44 LYS cc_start: 0.7715 (mmtt) cc_final: 0.6915 (tppt) outliers start: 24 outliers final: 17 residues processed: 166 average time/residue: 0.7711 time to fit residues: 179.0629 Evaluate side-chains 161 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 75 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128735 restraints weight = 52600.978| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.86 r_work: 0.3381 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14743 Z= 0.158 Angle : 0.514 4.570 19911 Z= 0.274 Chirality : 0.036 0.146 2309 Planarity : 0.004 0.047 2547 Dihedral : 4.001 24.933 1945 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 12.57 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.20), residues: 1817 helix: 2.20 (0.16), residues: 1103 sheet: -0.17 (0.27), residues: 300 loop : -0.61 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 122 HIS 0.016 0.001 HIS H 86 PHE 0.014 0.001 PHE F 71 TYR 0.014 0.001 TYR F 40 ARG 0.005 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 981) hydrogen bonds : angle 4.27149 ( 2844) covalent geometry : bond 0.00370 (14743) covalent geometry : angle 0.51426 (19911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ARG cc_start: 0.7520 (mmt180) cc_final: 0.7308 (mmt-90) REVERT: D 8 ASP cc_start: 0.8160 (m-30) cc_final: 0.7912 (m-30) REVERT: E 25 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7634 (mm) REVERT: E 65 ARG cc_start: 0.6440 (mtm-85) cc_final: 0.4222 (mmt-90) REVERT: E 81 GLN cc_start: 0.6939 (mt0) cc_final: 0.6541 (tt0) REVERT: F 35 CYS cc_start: 0.8564 (t) cc_final: 0.8131 (m) REVERT: H 86 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6586 (m170) REVERT: H 154 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7866 (mmtp) REVERT: I 29 GLN cc_start: 0.7525 (mt0) cc_final: 0.7140 (tm-30) REVERT: J 36 ARG cc_start: 0.7378 (tpp-160) cc_final: 0.6957 (tpt90) REVERT: J 44 LYS cc_start: 0.7732 (mmtt) cc_final: 0.6919 (tppt) REVERT: J 165 ASN cc_start: 0.7625 (m110) cc_final: 0.7391 (m110) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.6789 time to fit residues: 155.6569 Evaluate side-chains 163 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130118 restraints weight = 52182.263| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.63 r_work: 0.3428 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14743 Z= 0.121 Angle : 0.497 4.883 19911 Z= 0.264 Chirality : 0.035 0.142 2309 Planarity : 0.004 0.047 2547 Dihedral : 3.934 24.476 1945 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.30 % Allowed : 12.82 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.20), residues: 1817 helix: 2.30 (0.16), residues: 1103 sheet: -0.14 (0.27), residues: 301 loop : -0.58 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 122 HIS 0.010 0.001 HIS H 86 PHE 0.013 0.001 PHE F 71 TYR 0.013 0.001 TYR F 40 ARG 0.007 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 981) hydrogen bonds : angle 4.20800 ( 2844) covalent geometry : bond 0.00275 (14743) covalent geometry : angle 0.49727 (19911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7512 (tm-30) REVERT: D 2 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7385 (mmt-90) REVERT: D 8 ASP cc_start: 0.8111 (m-30) cc_final: 0.7859 (m-30) REVERT: D 128 MET cc_start: 0.7492 (mmt) cc_final: 0.6969 (mtp) REVERT: E 25 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7617 (mm) REVERT: E 65 ARG cc_start: 0.6367 (mtm-85) cc_final: 0.4132 (mmt-90) REVERT: E 81 GLN cc_start: 0.6877 (mt0) cc_final: 0.6485 (tt0) REVERT: F 35 CYS cc_start: 0.8593 (t) cc_final: 0.8124 (m) REVERT: H 86 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6526 (m170) REVERT: H 154 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7807 (mmtp) REVERT: I 25 ARG cc_start: 0.6501 (mmt90) cc_final: 0.6178 (mmt90) REVERT: I 29 GLN cc_start: 0.7516 (mt0) cc_final: 0.7129 (tm-30) REVERT: J 36 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6954 (tpt90) REVERT: J 44 LYS cc_start: 0.7720 (mmtt) cc_final: 0.6905 (tppt) REVERT: J 165 ASN cc_start: 0.7555 (m110) cc_final: 0.7299 (m110) outliers start: 21 outliers final: 19 residues processed: 162 average time/residue: 0.6913 time to fit residues: 157.8435 Evaluate side-chains 164 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 86 HIS Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 chunk 170 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.202534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131389 restraints weight = 52848.082| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.76 r_work: 0.3434 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14743 Z= 0.112 Angle : 0.486 4.967 19911 Z= 0.257 Chirality : 0.035 0.193 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.855 24.022 1945 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.24 % Allowed : 13.07 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 1817 helix: 2.39 (0.16), residues: 1104 sheet: -0.09 (0.27), residues: 301 loop : -0.56 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 122 HIS 0.019 0.001 HIS H 86 PHE 0.012 0.001 PHE F 71 TYR 0.013 0.001 TYR F 40 ARG 0.007 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 981) hydrogen bonds : angle 4.16059 ( 2844) covalent geometry : bond 0.00252 (14743) covalent geometry : angle 0.48622 (19911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19113.80 seconds wall clock time: 325 minutes 52.48 seconds (19552.48 seconds total)