Starting phenix.real_space_refine on Mon Aug 25 15:01:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2r_28825/08_2025/8f2r_28825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2r_28825/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f2r_28825/08_2025/8f2r_28825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2r_28825/08_2025/8f2r_28825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f2r_28825/08_2025/8f2r_28825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2r_28825/08_2025/8f2r_28825.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.11, per 1000 atoms: 0.17 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: 2.86 Conformation dependent library (CDL) restraints added in 905.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 6.67 Time building geometry restraints manager: 3.96 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: 4.240 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: 0.150 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (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 ARG 0.024 0.003 ARG D 127 TYR 0.031 0.005 TYR C 134 PHE 0.021 0.003 PHE G 96 TRP 0.026 0.005 TRP E 148 HIS 0.009 0.002 HIS J 181 Details of bonding type rmsd covalent geometry : bond 0.00398 (14743) covalent geometry : angle 0.79653 (19911) hydrogen bonds : bond 0.13029 ( 981) hydrogen bonds : angle 6.19719 ( 2844) *********************** 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 : 0.834 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: 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: 0.4001 time to fit residues: 104.7102 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 : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** H 25 HIS H 81 GLN I 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.214602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148664 restraints weight = 52054.362| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.65 r_work: 0.3629 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14743 Z= 0.193 Angle : 0.614 5.323 19911 Z= 0.332 Chirality : 0.039 0.184 2309 Planarity : 0.005 0.066 2547 Dihedral : 4.786 24.234 1945 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.43 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 10.77 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 1817 helix: 1.39 (0.15), residues: 1098 sheet: 0.40 (0.28), residues: 297 loop : 0.44 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 125 TYR 0.023 0.002 TYR F 40 PHE 0.018 0.002 PHE E 155 TRP 0.016 0.002 TRP A 115 HIS 0.007 0.002 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00443 (14743) covalent geometry : angle 0.61416 (19911) hydrogen bonds : bond 0.05008 ( 981) hydrogen bonds : angle 4.91296 ( 2844) *********************** 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 182 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.556 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 76 MET cc_start: 0.7486 (mtp) cc_final: 0.7260 (mtp) REVERT: E 36 MET cc_start: 0.8291 (ttp) cc_final: 0.8000 (tmm) REVERT: E 65 ARG cc_start: 0.5700 (mtm-85) cc_final: 0.4214 (mmt180) REVERT: E 81 GLN cc_start: 0.6962 (mt0) cc_final: 0.6665 (tt0) REVERT: G 148 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8742 (p) REVERT: H 34 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7356 (mtm-85) REVERT: I 92 GLN cc_start: 0.5495 (mp10) cc_final: 0.5086 (mm-40) REVERT: J 44 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7271 (tppt) REVERT: J 116 MET cc_start: 0.7860 (mtt) cc_final: 0.7615 (mtp) REVERT: J 144 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (tp40) outliers start: 18 outliers final: 11 residues processed: 178 average time/residue: 0.3397 time to fit residues: 84.3847 Evaluate side-chains 160 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 141 LEU Chi-restraints excluded: chain J residue 144 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 106 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.215152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146299 restraints weight = 53014.566| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.67 r_work: 0.3646 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14743 Z= 0.143 Angle : 0.523 5.048 19911 Z= 0.281 Chirality : 0.037 0.168 2309 Planarity : 0.004 0.051 2547 Dihedral : 4.392 23.715 1945 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 1.49 % Allowed : 10.71 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1817 helix: 1.81 (0.15), residues: 1103 sheet: 0.39 (0.28), residues: 291 loop : 0.27 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 158 TYR 0.019 0.001 TYR F 40 PHE 0.016 0.001 PHE G 141 TRP 0.011 0.001 TRP D 14 HIS 0.005 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00318 (14743) covalent geometry : angle 0.52332 (19911) hydrogen bonds : bond 0.04400 ( 981) hydrogen bonds : angle 4.54697 ( 2844) *********************** 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 177 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.822 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: 0.6076 (mtm-85) cc_final: 0.4001 (mmt-90) REVERT: E 81 GLN cc_start: 0.6797 (mt0) cc_final: 0.6507 (tt0) REVERT: H 34 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7316 (mtm-85) REVERT: I 29 GLN cc_start: 0.7575 (mt0) cc_final: 0.7140 (tm-30) REVERT: I 91 HIS cc_start: 0.7504 (m-70) cc_final: 0.7273 (m-70) REVERT: J 44 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7200 (tppt) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 0.3627 time to fit residues: 85.7615 Evaluate side-chains 160 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 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 H residue 57 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 50 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** J 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.211847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145955 restraints weight = 51069.649| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.63 r_work: 0.3597 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14743 Z= 0.142 Angle : 0.518 5.990 19911 Z= 0.276 Chirality : 0.036 0.163 2309 Planarity : 0.004 0.045 2547 Dihedral : 4.226 29.734 1945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Rotamer: Outliers : 1.73 % Allowed : 10.71 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.20), residues: 1817 helix: 2.01 (0.15), residues: 1103 sheet: 0.22 (0.27), residues: 292 loop : 0.08 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 36 TYR 0.017 0.001 TYR F 40 PHE 0.015 0.001 PHE G 141 TRP 0.012 0.001 TRP D 14 HIS 0.007 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00327 (14743) covalent geometry : angle 0.51788 (19911) hydrogen bonds : bond 0.04080 ( 981) hydrogen bonds : angle 4.36973 ( 2844) *********************** 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 182 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.715 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: 0.4849 (mtm-85) cc_final: 0.4572 (ttp80) REVERT: C 99 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7057 (tp) REVERT: D 139 ASP cc_start: 0.8629 (p0) cc_final: 0.8352 (p0) REVERT: E 65 ARG cc_start: 0.6173 (mtm-85) cc_final: 0.4153 (mmt180) REVERT: E 81 GLN cc_start: 0.6892 (mt0) cc_final: 0.6585 (tt0) REVERT: G 148 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8929 (p) REVERT: H 34 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7360 (mtm-85) REVERT: H 53 HIS cc_start: 0.7144 (m-70) cc_final: 0.6755 (m-70) REVERT: H 154 LYS cc_start: 0.8297 (mmmt) cc_final: 0.8016 (mmtp) REVERT: I 29 GLN cc_start: 0.7590 (mt0) cc_final: 0.7162 (tm-30) REVERT: J 44 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7088 (tppt) outliers start: 28 outliers final: 21 residues processed: 175 average time/residue: 0.3497 time to fit residues: 85.8281 Evaluate side-chains 176 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 146 GLU 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 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 135 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 0.0570 chunk 153 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 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 = 0.4512 r_free = 0.4512 target = 0.210201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142228 restraints weight = 51519.556| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.49 r_work: 0.3598 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14743 Z= 0.141 Angle : 0.501 4.614 19911 Z= 0.267 Chirality : 0.036 0.154 2309 Planarity : 0.004 0.046 2547 Dihedral : 4.082 24.875 1945 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 1.73 % Allowed : 11.46 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.20), residues: 1817 helix: 2.10 (0.16), residues: 1109 sheet: 0.20 (0.27), residues: 291 loop : -0.05 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 158 TYR 0.016 0.001 TYR F 40 PHE 0.014 0.001 PHE G 141 TRP 0.017 0.002 TRP H 46 HIS 0.007 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00326 (14743) covalent geometry : angle 0.50063 (19911) hydrogen bonds : bond 0.04046 ( 981) hydrogen bonds : angle 4.27869 ( 2844) *********************** 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 187 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.619 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: 0.4944 (mtm-85) cc_final: 0.4638 (ttp80) REVERT: B 138 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8313 (ttt-90) REVERT: E 25 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7429 (mm) REVERT: E 65 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.4225 (mmp-170) REVERT: E 81 GLN cc_start: 0.6888 (mt0) cc_final: 0.6563 (tt0) REVERT: G 148 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8982 (p) REVERT: H 34 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7447 (mtm-85) REVERT: H 154 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8036 (mmtp) REVERT: I 29 GLN cc_start: 0.7550 (mt0) cc_final: 0.7129 (tm-30) REVERT: J 36 ARG cc_start: 0.7215 (tpp-160) cc_final: 0.6896 (tpt90) REVERT: J 44 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7046 (tppt) outliers start: 28 outliers final: 19 residues processed: 181 average time/residue: 0.3391 time to fit residues: 84.1077 Evaluate side-chains 170 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 138 ARG Chi-restraints excluded: chain B residue 142 GLN 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 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 125 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 34 ARG 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 141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 135 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4530 r_free = 0.4530 target = 0.211911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146268 restraints weight = 52853.177| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.55 r_work: 0.3588 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14743 Z= 0.123 Angle : 0.488 4.687 19911 Z= 0.259 Chirality : 0.035 0.137 2309 Planarity : 0.004 0.050 2547 Dihedral : 3.954 24.231 1945 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 1.55 % Allowed : 11.70 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.20), residues: 1817 helix: 2.26 (0.16), residues: 1103 sheet: 0.15 (0.28), residues: 292 loop : -0.08 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 191 TYR 0.014 0.001 TYR F 40 PHE 0.013 0.001 PHE G 141 TRP 0.016 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00282 (14743) covalent geometry : angle 0.48847 (19911) hydrogen bonds : bond 0.03755 ( 981) hydrogen bonds : angle 4.19199 ( 2844) *********************** 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 180 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.832 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: 0.4963 (mtm-85) cc_final: 0.4656 (ttp80) REVERT: C 99 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7220 (tp) REVERT: E 25 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7350 (mm) REVERT: E 65 ARG cc_start: 0.6355 (mtm-85) cc_final: 0.4300 (mmp-170) REVERT: E 170 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7720 (mtp85) REVERT: F 35 CYS cc_start: 0.8387 (t) cc_final: 0.8097 (m) REVERT: G 148 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8970 (p) REVERT: H 34 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7107 (mtm-85) REVERT: H 53 HIS cc_start: 0.7051 (m-70) cc_final: 0.6657 (m-70) REVERT: H 154 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7962 (mmtp) REVERT: I 29 GLN cc_start: 0.7473 (mt0) cc_final: 0.7157 (tm-30) REVERT: J 44 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7032 (tppt) REVERT: J 167 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6149 (mm-30) outliers start: 25 outliers final: 17 residues processed: 176 average time/residue: 0.3765 time to fit residues: 91.9502 Evaluate side-chains 166 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 143 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 96 optimal weight: 0.0370 chunk 150 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 I 191 GLN J 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.212020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143490 restraints weight = 52893.654| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.55 r_work: 0.3599 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14743 Z= 0.109 Angle : 0.473 4.686 19911 Z= 0.250 Chirality : 0.035 0.135 2309 Planarity : 0.004 0.043 2547 Dihedral : 3.833 23.517 1945 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 11.76 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.20), residues: 1817 helix: 2.40 (0.16), residues: 1103 sheet: 0.19 (0.28), residues: 292 loop : -0.09 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 191 TYR 0.012 0.001 TYR F 40 PHE 0.012 0.001 PHE F 71 TRP 0.016 0.001 TRP H 46 HIS 0.005 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00245 (14743) covalent geometry : angle 0.47331 (19911) hydrogen bonds : bond 0.03545 ( 981) hydrogen bonds : angle 4.10439 ( 2844) *********************** 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 177 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.843 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: 0.5124 (mtm-85) cc_final: 0.4844 (tmm-80) REVERT: C 99 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7221 (tp) REVERT: D 128 MET cc_start: 0.7514 (mmt) cc_final: 0.6795 (mtp) REVERT: E 25 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7413 (mm) REVERT: E 65 ARG cc_start: 0.6380 (mtm-85) cc_final: 0.4343 (mmp-170) REVERT: E 170 ARG cc_start: 0.8223 (ptp-110) cc_final: 0.7728 (mtp85) REVERT: F 35 CYS cc_start: 0.8361 (t) cc_final: 0.8143 (m) REVERT: H 34 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7266 (mtm-85) REVERT: H 154 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7972 (mmtp) REVERT: I 29 GLN cc_start: 0.7538 (mt0) cc_final: 0.7171 (tm-30) REVERT: J 44 LYS cc_start: 0.7715 (mmtt) cc_final: 0.6919 (tppt) outliers start: 25 outliers final: 20 residues processed: 171 average time/residue: 0.3787 time to fit residues: 89.6929 Evaluate side-chains 167 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 C residue 155 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 139 ASP 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 H residue 34 ARG Chi-restraints excluded: chain I residue 144 VAL 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 1 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN H 53 HIS J 39 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.203179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132401 restraints weight = 52007.128| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.74 r_work: 0.3399 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14743 Z= 0.174 Angle : 0.531 4.648 19911 Z= 0.284 Chirality : 0.037 0.150 2309 Planarity : 0.004 0.052 2547 Dihedral : 3.976 26.277 1945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Rotamer: Outliers : 1.55 % Allowed : 12.14 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.20), residues: 1817 helix: 2.21 (0.16), residues: 1105 sheet: 0.01 (0.27), residues: 299 loop : -0.32 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 38 TYR 0.017 0.001 TYR F 40 PHE 0.014 0.002 PHE F 71 TRP 0.014 0.002 TRP H 46 HIS 0.009 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00412 (14743) covalent geometry : angle 0.53083 (19911) hydrogen bonds : bond 0.04254 ( 981) hydrogen bonds : angle 4.26090 ( 2844) *********************** 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 174 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7670 (tp) REVERT: D 1 MET cc_start: 0.6037 (mmt) cc_final: 0.5742 (mmt) REVERT: D 128 MET cc_start: 0.7543 (mmt) cc_final: 0.7095 (mtp) REVERT: E 25 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7597 (mm) REVERT: E 65 ARG cc_start: 0.6425 (mtm-85) cc_final: 0.4308 (mmp-170) REVERT: E 81 GLN cc_start: 0.6913 (mt0) cc_final: 0.6502 (tt0) REVERT: E 170 ARG cc_start: 0.8308 (ptp-110) cc_final: 0.7662 (mtp85) REVERT: G 137 MET cc_start: 0.8341 (ttt) cc_final: 0.7929 (ttt) REVERT: H 34 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7433 (mtm-85) REVERT: H 154 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7894 (mmtp) REVERT: I 29 GLN cc_start: 0.7550 (mt0) cc_final: 0.7137 (tm-30) REVERT: I 55 GLU cc_start: 0.6016 (mp0) cc_final: 0.5557 (mp0) REVERT: J 44 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7002 (tppt) outliers start: 25 outliers final: 22 residues processed: 170 average time/residue: 0.3446 time to fit residues: 81.6698 Evaluate side-chains 170 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 18 GLN 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 H residue 86 HIS Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 144 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 HIS J 39 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.204726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132372 restraints weight = 51913.066| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.44 r_work: 0.3463 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14743 Z= 0.112 Angle : 0.484 5.048 19911 Z= 0.256 Chirality : 0.035 0.139 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.883 25.294 1945 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 12.38 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 1817 helix: 2.37 (0.16), residues: 1106 sheet: 0.10 (0.28), residues: 299 loop : -0.28 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 110 TYR 0.014 0.001 TYR F 40 PHE 0.014 0.001 PHE G 141 TRP 0.013 0.001 TRP H 46 HIS 0.005 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00248 (14743) covalent geometry : angle 0.48369 (19911) hydrogen bonds : bond 0.03748 ( 981) hydrogen bonds : angle 4.14115 ( 2844) *********************** 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 173 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6110 (mmt) cc_final: 0.5739 (mmt) REVERT: D 2 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7067 (mmt-90) REVERT: D 128 MET cc_start: 0.7365 (mmt) cc_final: 0.6981 (mtp) REVERT: E 25 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7589 (mm) REVERT: E 65 ARG cc_start: 0.6273 (mtm-85) cc_final: 0.4217 (mmp-170) REVERT: E 81 GLN cc_start: 0.6803 (mt0) cc_final: 0.6415 (tt0) REVERT: E 170 ARG cc_start: 0.8292 (ptp-110) cc_final: 0.7669 (mtp85) REVERT: F 35 CYS cc_start: 0.8450 (t) cc_final: 0.8022 (m) REVERT: G 137 MET cc_start: 0.8287 (ttt) cc_final: 0.7865 (ttt) REVERT: H 34 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7337 (mtm-85) REVERT: H 154 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7828 (mmtp) REVERT: I 29 GLN cc_start: 0.7522 (mt0) cc_final: 0.7139 (tm-30) REVERT: I 55 GLU cc_start: 0.6077 (mp0) cc_final: 0.5653 (mp0) REVERT: J 44 LYS cc_start: 0.7680 (mmtt) cc_final: 0.6982 (tppt) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.3830 time to fit residues: 89.3215 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 : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 165 GLU 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 155 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 139 ASP 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 144 VAL 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 0 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131425 restraints weight = 52836.870| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.77 r_work: 0.3434 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14743 Z= 0.129 Angle : 0.490 5.028 19911 Z= 0.260 Chirality : 0.036 0.216 2309 Planarity : 0.004 0.047 2547 Dihedral : 3.820 24.582 1945 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 1.36 % Allowed : 12.57 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.20), residues: 1817 helix: 2.43 (0.16), residues: 1105 sheet: 0.11 (0.27), residues: 298 loop : -0.34 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 193 TYR 0.014 0.001 TYR F 40 PHE 0.013 0.001 PHE F 71 TRP 0.014 0.001 TRP H 46 HIS 0.006 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00300 (14743) covalent geometry : angle 0.49050 (19911) hydrogen bonds : bond 0.03746 ( 981) hydrogen bonds : angle 4.09950 ( 2844) ********************** 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 173 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ARG cc_start: 0.7583 (mmt180) cc_final: 0.7379 (mmt-90) REVERT: D 128 MET cc_start: 0.7464 (mmt) cc_final: 0.7135 (mtp) REVERT: E 25 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7614 (mm) REVERT: E 65 ARG cc_start: 0.6350 (mtm-85) cc_final: 0.4247 (mmp-170) REVERT: E 81 GLN cc_start: 0.6840 (mt0) cc_final: 0.6401 (tt0) REVERT: E 170 ARG cc_start: 0.8354 (ptp-110) cc_final: 0.7668 (mtp85) REVERT: F 35 CYS cc_start: 0.8576 (t) cc_final: 0.8118 (m) REVERT: G 137 MET cc_start: 0.8383 (ttt) cc_final: 0.7932 (ttt) REVERT: H 34 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6976 (mtm-85) REVERT: H 154 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7842 (mmtp) REVERT: I 29 GLN cc_start: 0.7486 (mt0) cc_final: 0.7061 (tm-30) REVERT: I 55 GLU cc_start: 0.6114 (mp0) cc_final: 0.5618 (mp0) REVERT: J 44 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6989 (tppt) outliers start: 22 outliers final: 19 residues processed: 171 average time/residue: 0.3749 time to fit residues: 87.7918 Evaluate side-chains 168 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 148 SER Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 59 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 HIS ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.204159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135862 restraints weight = 52150.806| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.73 r_work: 0.3424 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 14743 Z= 0.152 Angle : 0.723 59.200 19911 Z= 0.421 Chirality : 0.035 0.178 2309 Planarity : 0.004 0.046 2547 Dihedral : 3.815 24.666 1945 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.30 % Allowed : 12.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.20), residues: 1817 helix: 2.44 (0.16), residues: 1105 sheet: 0.11 (0.27), residues: 298 loop : -0.34 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 110 TYR 0.013 0.001 TYR F 40 PHE 0.013 0.001 PHE F 71 TRP 0.012 0.001 TRP H 46 HIS 0.007 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00330 (14743) covalent geometry : angle 0.72340 (19911) hydrogen bonds : bond 0.03756 ( 981) hydrogen bonds : angle 4.09717 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9926.13 seconds wall clock time: 168 minutes 37.04 seconds (10117.04 seconds total)