Starting phenix.real_space_refine on Sun Aug 24 10:31:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyj_18755/08_2025/8qyj_18755.map" } resolution = 2.73 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= 0.008 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12336 2.51 5 N 3306 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 19402 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1841 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1847 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1848 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1886 Unusual residues: {'ACE': 1} Classifications: {'peptide': 239, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1787 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 408 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1933 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1909 Unusual residues: {'ACE': 1} Classifications: {'peptide': 247, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 512 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Time building chain proxies: 3.45, per 1000 atoms: 0.18 Number of scatterers: 19402 At special positions: 0 Unit cell: (123.424, 141.299, 133.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3646 8.00 N 3306 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 605.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4682 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 40.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.644A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.681A pdb=" N HIS A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.930A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.536A pdb=" N ALA A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.601A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.610A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 248 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.599A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 60' Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.624A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 201 through 204 removed outlier: 4.391A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 221 through 241 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 84 through 104 removed outlier: 4.497A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.836A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.934A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'E' and resid 3 through 7 removed outlier: 4.074A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.907A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 78 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.008A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 179 removed outlier: 3.822A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.661A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.602A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.530A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 201 removed outlier: 4.358A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.553A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 3.558A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.720A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.794A pdb=" N LYS G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 182 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.726A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'I' and resid 35 through 45 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.715A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.580A pdb=" N SER I 183 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 265 through 277 removed outlier: 4.066A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 99 through 114 removed outlier: 3.575A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.554A pdb=" N SER J 136 " --> pdb=" O GLN J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.964A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 114 Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.533A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 90 removed outlier: 5.950A pdb=" N PHE L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 119 removed outlier: 3.703A pdb=" N GLU L 114 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 103 through 119 Processing helix chain 'M' and resid 120 through 123 removed outlier: 3.613A pdb=" N PHE M 123 " --> pdb=" O PRO M 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 120 through 123' Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.558A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 157 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.513A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.526A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 5.354A pdb=" N GLY E 216 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLU E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.622A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.507A pdb=" N GLY E 76 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 166 removed outlier: 4.042A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.642A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.575A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.964A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.534A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU J 90 " --> pdb=" O PRO J 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.534A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU J 90 " --> pdb=" O PRO J 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 78 through 81 removed outlier: 5.032A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY K 145 " --> pdb=" O HIS K 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 8 through 16 removed outlier: 4.224A pdb=" N ILE L 8 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE L 32 " --> pdb=" O LEU L 96 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA L 98 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL L 34 " --> pdb=" O ALA L 98 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA L 100 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL L 36 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU L 45 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 13 through 21 removed outlier: 3.626A pdb=" N SER M 36 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU M 37 " --> pdb=" O PHE M 92 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER M 94 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 39 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU M 50 " --> pdb=" O LEU M 67 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6323 1.34 - 1.46: 2532 1.46 - 1.57: 10719 1.57 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 19748 Sorted by residual: bond pdb=" C ACE D 0 " pdb=" O ACE D 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C ACE J 0 " pdb=" O ACE J 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CD GLU M 117 " pdb=" OE1 GLU M 117 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CA ASN K 83 " pdb=" CB ASN K 83 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.01e+00 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 26549 2.14 - 4.27: 149 4.27 - 6.41: 14 6.41 - 8.55: 1 8.55 - 10.68: 1 Bond angle restraints: 26714 Sorted by residual: angle pdb=" N GLU M 117 " pdb=" CA GLU M 117 " pdb=" CB GLU M 117 " ideal model delta sigma weight residual 110.40 116.35 -5.95 1.63e+00 3.76e-01 1.33e+01 angle pdb=" N THR D 213 " pdb=" CA THR D 213 " pdb=" C THR D 213 " ideal model delta sigma weight residual 114.56 109.94 4.62 1.27e+00 6.20e-01 1.32e+01 angle pdb=" C MET M 116 " pdb=" N GLU M 117 " pdb=" CA GLU M 117 " ideal model delta sigma weight residual 121.14 115.02 6.12 1.75e+00 3.27e-01 1.22e+01 angle pdb=" C PRO K 82 " pdb=" N ASN K 83 " pdb=" CA ASN K 83 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N GLU C 237 " pdb=" CA GLU C 237 " pdb=" CB GLU C 237 " ideal model delta sigma weight residual 110.28 115.10 -4.82 1.55e+00 4.16e-01 9.68e+00 ... (remaining 26709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10885 17.57 - 35.14: 884 35.14 - 52.71: 129 52.71 - 70.28: 36 70.28 - 87.86: 24 Dihedral angle restraints: 11958 sinusoidal: 4710 harmonic: 7248 Sorted by residual: dihedral pdb=" CA TRP F 216 " pdb=" C TRP F 216 " pdb=" N VAL F 217 " pdb=" CA VAL F 217 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN D 104 " pdb=" C ASN D 104 " pdb=" N GLU D 105 " pdb=" CA GLU D 105 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP E 94 " pdb=" CB ASP E 94 " pdb=" CG ASP E 94 " pdb=" OD1 ASP E 94 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 11955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1941 0.029 - 0.058: 710 0.058 - 0.088: 211 0.088 - 0.117: 191 0.117 - 0.146: 26 Chirality restraints: 3079 Sorted by residual: chirality pdb=" CA GLU C 237 " pdb=" N GLU C 237 " pdb=" C GLU C 237 " pdb=" CB GLU C 237 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE K 84 " pdb=" N ILE K 84 " pdb=" C ILE K 84 " pdb=" CB ILE K 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CB THR D 113 " pdb=" CA THR D 113 " pdb=" OG1 THR D 113 " pdb=" CG2 THR D 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 3076 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.017 2.00e-02 2.50e+03 1.71e-02 7.28e+00 pdb=" CG TRP F 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 16 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO F 17 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 17 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 17 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO K 82 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C PRO K 82 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO K 82 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN K 83 " 0.010 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3135 2.77 - 3.30: 16805 3.30 - 3.83: 29800 3.83 - 4.37: 34705 4.37 - 4.90: 64645 Nonbonded interactions: 149090 Sorted by model distance: nonbonded pdb=" O ARG K 124 " pdb=" NE2 GLN K 128 " model vdw 2.235 3.120 nonbonded pdb=" OG SER E 33 " pdb=" NZ LYS E 62 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP B 151 " pdb=" OG SER B 153 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.248 3.040 nonbonded pdb=" OG SER L 29 " pdb=" O PRO M 45 " model vdw 2.259 3.040 ... (remaining 149085 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: 1.760 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 15.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19748 Z= 0.096 Angle : 0.442 10.682 26714 Z= 0.238 Chirality : 0.041 0.146 3079 Planarity : 0.004 0.044 3404 Dihedral : 13.648 87.855 7276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.76 (0.17), residues: 2456 helix: 2.87 (0.18), residues: 889 sheet: 0.99 (0.23), residues: 550 loop : -0.29 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 106 TYR 0.007 0.001 TYR B 156 PHE 0.013 0.001 PHE G 9 TRP 0.045 0.001 TRP F 216 HIS 0.003 0.000 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00207 (19748) covalent geometry : angle 0.44158 (26714) hydrogen bonds : bond 0.17446 ( 1004) hydrogen bonds : angle 6.04160 ( 2925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.685 Fit side-chains REVERT: F 171 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7028 (tp-100) REVERT: M 121 GLU cc_start: 0.7673 (pm20) cc_final: 0.7403 (pm20) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.5999 time to fit residues: 190.3130 Evaluate side-chains 224 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 69 ASN B 84 ASN B 155 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN G 224 ASN I 280 ASN J 152 GLN J 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082857 restraints weight = 30184.553| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.39 r_work: 0.2929 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19748 Z= 0.119 Angle : 0.494 9.880 26714 Z= 0.266 Chirality : 0.042 0.150 3079 Planarity : 0.004 0.047 3404 Dihedral : 3.799 18.091 2690 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.47 % Allowed : 7.26 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.85 (0.17), residues: 2456 helix: 3.00 (0.18), residues: 890 sheet: 1.24 (0.22), residues: 545 loop : -0.43 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 169 TYR 0.012 0.001 TYR B 136 PHE 0.016 0.001 PHE A 173 TRP 0.026 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00275 (19748) covalent geometry : angle 0.49398 (26714) hydrogen bonds : bond 0.04593 ( 1004) hydrogen bonds : angle 4.52687 ( 2925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.590 Fit side-chains REVERT: A 179 ASN cc_start: 0.8119 (t0) cc_final: 0.7899 (t0) REVERT: D 1 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: D 207 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: E 203 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: F 28 MET cc_start: 0.8920 (mtp) cc_final: 0.8642 (mtm) REVERT: F 171 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7224 (tp-100) REVERT: G 112 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8580 (p0) REVERT: J 40 ASN cc_start: 0.8701 (t0) cc_final: 0.8460 (t0) REVERT: K 97 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6342 (ttm) REVERT: M 121 GLU cc_start: 0.7927 (pm20) cc_final: 0.7543 (pm20) outliers start: 31 outliers final: 8 residues processed: 235 average time/residue: 0.6726 time to fit residues: 175.8718 Evaluate side-chains 223 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain M residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 142 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 84 ASN B 155 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN I 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.077897 restraints weight = 29608.094| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.50 r_work: 0.2789 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19748 Z= 0.136 Angle : 0.500 10.331 26714 Z= 0.268 Chirality : 0.043 0.165 3079 Planarity : 0.004 0.049 3404 Dihedral : 3.981 20.103 2690 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 9.31 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.76 (0.17), residues: 2456 helix: 2.93 (0.18), residues: 897 sheet: 1.20 (0.22), residues: 542 loop : -0.50 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 164 TYR 0.010 0.001 TYR B 136 PHE 0.014 0.001 PHE A 173 TRP 0.020 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00325 (19748) covalent geometry : angle 0.49995 (26714) hydrogen bonds : bond 0.04830 ( 1004) hydrogen bonds : angle 4.32435 ( 2925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.812 Fit side-chains REVERT: A 179 ASN cc_start: 0.7926 (t0) cc_final: 0.7665 (t0) REVERT: B 151 ASP cc_start: 0.8213 (p0) cc_final: 0.7957 (p0) REVERT: D 10 ARG cc_start: 0.8602 (mtt180) cc_final: 0.7712 (mtm110) REVERT: D 148 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: D 207 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: F 171 GLN cc_start: 0.7579 (tp-100) cc_final: 0.6955 (tp-100) REVERT: G 112 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (p0) REVERT: G 130 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: H 81 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7736 (mtp) REVERT: I 40 GLN cc_start: 0.7671 (mm110) cc_final: 0.7435 (mm110) REVERT: M 121 GLU cc_start: 0.7911 (pm20) cc_final: 0.7465 (pm20) outliers start: 33 outliers final: 10 residues processed: 228 average time/residue: 0.7252 time to fit residues: 183.5548 Evaluate side-chains 223 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 47 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN I 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.080426 restraints weight = 29433.504| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.49 r_work: 0.2857 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19748 Z= 0.094 Angle : 0.447 10.385 26714 Z= 0.242 Chirality : 0.041 0.155 3079 Planarity : 0.004 0.049 3404 Dihedral : 3.774 17.836 2690 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.28 % Allowed : 10.35 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.89 (0.17), residues: 2456 helix: 3.03 (0.18), residues: 897 sheet: 1.25 (0.22), residues: 546 loop : -0.41 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 164 TYR 0.008 0.001 TYR B 136 PHE 0.012 0.001 PHE A 173 TRP 0.014 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00209 (19748) covalent geometry : angle 0.44680 (26714) hydrogen bonds : bond 0.03573 ( 1004) hydrogen bonds : angle 4.09260 ( 2925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.799 Fit side-chains REVERT: A 179 ASN cc_start: 0.7943 (t0) cc_final: 0.7687 (t0) REVERT: D 166 ASP cc_start: 0.9045 (m-30) cc_final: 0.8801 (m-30) REVERT: D 207 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: F 28 MET cc_start: 0.8526 (mtp) cc_final: 0.8208 (mtm) REVERT: F 171 GLN cc_start: 0.7474 (tp-100) cc_final: 0.6858 (tp-100) REVERT: H 81 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: M 121 GLU cc_start: 0.7914 (pm20) cc_final: 0.7472 (pm20) outliers start: 27 outliers final: 12 residues processed: 228 average time/residue: 0.6995 time to fit residues: 177.5927 Evaluate side-chains 220 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 84 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN F 64 ASN F 181 GLN G 224 ASN I 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.080165 restraints weight = 29334.805| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.50 r_work: 0.2853 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19748 Z= 0.098 Angle : 0.454 10.361 26714 Z= 0.244 Chirality : 0.041 0.166 3079 Planarity : 0.004 0.050 3404 Dihedral : 3.726 16.962 2690 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.61 % Allowed : 11.35 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.91 (0.17), residues: 2456 helix: 3.05 (0.18), residues: 898 sheet: 1.26 (0.22), residues: 546 loop : -0.40 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 164 TYR 0.009 0.001 TYR B 136 PHE 0.012 0.001 PHE A 173 TRP 0.011 0.001 TRP F 216 HIS 0.003 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00222 (19748) covalent geometry : angle 0.45424 (26714) hydrogen bonds : bond 0.03675 ( 1004) hydrogen bonds : angle 4.03036 ( 2925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.500 Fit side-chains REVERT: A 179 ASN cc_start: 0.7914 (t0) cc_final: 0.7645 (t0) REVERT: D 166 ASP cc_start: 0.9052 (m-30) cc_final: 0.8807 (m-30) REVERT: D 207 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: E 203 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: F 28 MET cc_start: 0.8523 (mtp) cc_final: 0.8166 (mtm) REVERT: F 171 GLN cc_start: 0.7484 (tp-100) cc_final: 0.6862 (tp-100) REVERT: G 112 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8338 (p0) REVERT: H 81 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7580 (mtp) REVERT: I 283 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (mt0) REVERT: K 128 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5427 (mp10) REVERT: M 117 GLU cc_start: 0.7639 (tp30) cc_final: 0.7068 (mp0) REVERT: M 121 GLU cc_start: 0.7926 (pm20) cc_final: 0.7481 (pm20) outliers start: 34 outliers final: 17 residues processed: 225 average time/residue: 0.6292 time to fit residues: 157.7899 Evaluate side-chains 225 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 83 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 chunk 139 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 84 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.081368 restraints weight = 29285.237| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.49 r_work: 0.2875 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.002 0.030 19748 Z= 0.089 Angle : 0.438 10.475 26714 Z= 0.237 Chirality : 0.041 0.155 3079 Planarity : 0.004 0.050 3404 Dihedral : 3.633 16.093 2690 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.38 % Allowed : 12.01 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.99 (0.17), residues: 2456 helix: 3.10 (0.18), residues: 898 sheet: 1.28 (0.22), residues: 547 loop : -0.33 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 43 TYR 0.008 0.001 TYR I 66 PHE 0.011 0.001 PHE A 173 TRP 0.009 0.001 TRP F 216 HIS 0.003 0.000 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00195 (19748) covalent geometry : angle 0.43836 (26714) hydrogen bonds : bond 0.03233 ( 1004) hydrogen bonds : angle 3.93397 ( 2925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.779 Fit side-chains REVERT: A 179 ASN cc_start: 0.7886 (t0) cc_final: 0.7626 (t0) REVERT: D 10 ARG cc_start: 0.8572 (mtt180) cc_final: 0.7610 (mtp180) REVERT: D 166 ASP cc_start: 0.9042 (m-30) cc_final: 0.8793 (m-30) REVERT: D 207 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: E 4 ASN cc_start: 0.8211 (t0) cc_final: 0.7626 (m110) REVERT: E 203 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7230 (mt0) REVERT: F 28 MET cc_start: 0.8496 (mtp) cc_final: 0.8134 (mtm) REVERT: F 171 GLN cc_start: 0.7475 (tp-100) cc_final: 0.6869 (tp-100) REVERT: H 81 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: M 117 GLU cc_start: 0.7629 (tp30) cc_final: 0.6983 (mp0) REVERT: M 121 GLU cc_start: 0.7927 (pm20) cc_final: 0.7482 (pm20) outliers start: 29 outliers final: 17 residues processed: 225 average time/residue: 0.6697 time to fit residues: 168.2921 Evaluate side-chains 222 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 84 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN K 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.076742 restraints weight = 29472.107| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.47 r_work: 0.2767 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19748 Z= 0.177 Angle : 0.541 9.680 26714 Z= 0.291 Chirality : 0.044 0.179 3079 Planarity : 0.005 0.052 3404 Dihedral : 4.069 19.697 2690 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.99 % Allowed : 12.06 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.69 (0.17), residues: 2456 helix: 2.86 (0.17), residues: 897 sheet: 1.23 (0.22), residues: 538 loop : -0.57 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.014 0.001 TYR B 136 PHE 0.014 0.002 PHE E 97 TRP 0.010 0.001 TRP G 101 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00441 (19748) covalent geometry : angle 0.54135 (26714) hydrogen bonds : bond 0.05435 ( 1004) hydrogen bonds : angle 4.24182 ( 2925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.814 Fit side-chains REVERT: A 179 ASN cc_start: 0.7919 (t0) cc_final: 0.7653 (t0) REVERT: D 207 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: E 186 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: E 203 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: F 28 MET cc_start: 0.8681 (mtp) cc_final: 0.8350 (mtm) REVERT: F 94 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7635 (tt0) REVERT: F 171 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7038 (tp-100) REVERT: G 112 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8556 (p0) REVERT: H 81 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7753 (mtp) REVERT: H 110 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: I 283 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: K 128 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5520 (mp10) REVERT: M 117 GLU cc_start: 0.7676 (tp30) cc_final: 0.7123 (mp0) REVERT: M 121 GLU cc_start: 0.7983 (pm20) cc_final: 0.7600 (pm20) outliers start: 42 outliers final: 20 residues processed: 229 average time/residue: 0.7249 time to fit residues: 184.2602 Evaluate side-chains 226 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 181 GLN G 224 ASN K 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.078250 restraints weight = 29386.354| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.48 r_work: 0.2808 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19748 Z= 0.123 Angle : 0.496 9.617 26714 Z= 0.267 Chirality : 0.042 0.161 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.958 19.135 2690 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.76 % Allowed : 12.68 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.74 (0.17), residues: 2456 helix: 2.93 (0.18), residues: 897 sheet: 1.21 (0.22), residues: 543 loop : -0.54 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 233 TYR 0.012 0.001 TYR B 136 PHE 0.013 0.001 PHE A 173 TRP 0.010 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00292 (19748) covalent geometry : angle 0.49570 (26714) hydrogen bonds : bond 0.04383 ( 1004) hydrogen bonds : angle 4.12771 ( 2925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.787 Fit side-chains REVERT: A 179 ASN cc_start: 0.7895 (t0) cc_final: 0.7642 (t0) REVERT: D 10 ARG cc_start: 0.8557 (mtt180) cc_final: 0.7693 (mtm110) REVERT: D 207 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: E 186 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: E 203 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: F 28 MET cc_start: 0.8673 (mtp) cc_final: 0.8363 (mtm) REVERT: F 94 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7606 (tt0) REVERT: F 171 GLN cc_start: 0.7630 (tp-100) cc_final: 0.6951 (tp-100) REVERT: H 81 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7743 (mtp) REVERT: H 110 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: K 128 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5531 (mp10) REVERT: M 117 GLU cc_start: 0.7668 (tp30) cc_final: 0.7068 (mp0) REVERT: M 121 GLU cc_start: 0.8013 (pm20) cc_final: 0.7568 (pm20) outliers start: 37 outliers final: 21 residues processed: 222 average time/residue: 0.6559 time to fit residues: 161.6503 Evaluate side-chains 224 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 59 optimal weight: 0.0970 chunk 187 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN K 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.080131 restraints weight = 29540.767| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.43 r_work: 0.2835 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19748 Z= 0.098 Angle : 0.465 9.817 26714 Z= 0.252 Chirality : 0.041 0.156 3079 Planarity : 0.004 0.051 3404 Dihedral : 3.795 17.703 2690 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.19 % Allowed : 13.39 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.86 (0.17), residues: 2456 helix: 3.02 (0.18), residues: 897 sheet: 1.26 (0.22), residues: 544 loop : -0.46 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 106 TYR 0.009 0.001 TYR B 136 PHE 0.014 0.001 PHE A 173 TRP 0.010 0.001 TRP I 149 HIS 0.003 0.000 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00219 (19748) covalent geometry : angle 0.46496 (26714) hydrogen bonds : bond 0.03554 ( 1004) hydrogen bonds : angle 4.00588 ( 2925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.763 Fit side-chains REVERT: A 179 ASN cc_start: 0.7932 (t0) cc_final: 0.7677 (t0) REVERT: D 10 ARG cc_start: 0.8563 (mtt180) cc_final: 0.7696 (mtm110) REVERT: D 65 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7356 (pp20) REVERT: D 166 ASP cc_start: 0.9106 (m-30) cc_final: 0.8870 (m-30) REVERT: D 207 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: E 186 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: E 203 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: F 28 MET cc_start: 0.8636 (mtp) cc_final: 0.8341 (mtm) REVERT: F 94 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7613 (tt0) REVERT: F 171 GLN cc_start: 0.7600 (tp-100) cc_final: 0.6930 (tp-100) REVERT: H 81 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7735 (mtp) REVERT: J 161 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7666 (tp30) REVERT: M 117 GLU cc_start: 0.7729 (tp30) cc_final: 0.7110 (mp0) REVERT: M 121 GLU cc_start: 0.8021 (pm20) cc_final: 0.7574 (pm20) outliers start: 25 outliers final: 18 residues processed: 218 average time/residue: 0.6853 time to fit residues: 166.4197 Evaluate side-chains 224 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN K 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.080818 restraints weight = 29419.749| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.49 r_work: 0.2841 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19748 Z= 0.093 Angle : 0.462 9.929 26714 Z= 0.249 Chirality : 0.041 0.153 3079 Planarity : 0.004 0.051 3404 Dihedral : 3.711 16.786 2690 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.23 % Allowed : 13.58 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.92 (0.17), residues: 2456 helix: 3.03 (0.18), residues: 899 sheet: 1.26 (0.22), residues: 547 loop : -0.38 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 43 TYR 0.008 0.001 TYR B 136 PHE 0.014 0.001 PHE A 173 TRP 0.010 0.001 TRP I 149 HIS 0.003 0.000 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00206 (19748) covalent geometry : angle 0.46152 (26714) hydrogen bonds : bond 0.03346 ( 1004) hydrogen bonds : angle 3.94837 ( 2925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.803 Fit side-chains REVERT: A 179 ASN cc_start: 0.7922 (t0) cc_final: 0.7691 (t0) REVERT: D 65 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7325 (pp20) REVERT: D 207 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: E 4 ASN cc_start: 0.8291 (t0) cc_final: 0.7702 (m110) REVERT: E 186 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: E 203 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: F 28 MET cc_start: 0.8591 (mtp) cc_final: 0.8201 (mtm) REVERT: F 94 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7621 (tt0) REVERT: F 171 GLN cc_start: 0.7568 (tp-100) cc_final: 0.6936 (tp-100) REVERT: H 81 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7719 (mtp) REVERT: I 283 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: J 161 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7660 (tp30) REVERT: K 127 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7488 (mtpp) REVERT: K 128 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5509 (mp10) REVERT: M 117 GLU cc_start: 0.7739 (tp30) cc_final: 0.7076 (mp0) REVERT: M 121 GLU cc_start: 0.7999 (pm20) cc_final: 0.7556 (pm20) outliers start: 26 outliers final: 17 residues processed: 220 average time/residue: 0.7176 time to fit residues: 175.8108 Evaluate side-chains 224 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 84 ASN B 146 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 224 ASN H 108 ASN K 83 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.075787 restraints weight = 29576.626| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.47 r_work: 0.2766 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19748 Z= 0.220 Angle : 0.595 9.253 26714 Z= 0.319 Chirality : 0.046 0.198 3079 Planarity : 0.005 0.053 3404 Dihedral : 4.254 20.604 2690 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.66 % Allowed : 13.15 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.51 (0.17), residues: 2456 helix: 2.71 (0.17), residues: 896 sheet: 1.25 (0.22), residues: 527 loop : -0.73 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 233 TYR 0.018 0.002 TYR B 136 PHE 0.015 0.002 PHE E 97 TRP 0.010 0.002 TRP G 101 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00556 (19748) covalent geometry : angle 0.59530 (26714) hydrogen bonds : bond 0.06141 ( 1004) hydrogen bonds : angle 4.34615 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6386.86 seconds wall clock time: 109 minutes 31.94 seconds (6571.94 seconds total)