Starting phenix.real_space_refine on Wed Jan 22 21:13:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyj_18755/01_2025/8qyj_18755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyj_18755/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyj_18755/01_2025/8qyj_18755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyj_18755/01_2025/8qyj_18755.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyj_18755/01_2025/8qyj_18755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyj_18755/01_2025/8qyj_18755.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'GLU:plan': 1, 'ARG: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: 11.06, per 1000 atoms: 0.57 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: 5.17 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.41 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: 6.06 Time building geometry restraints manager: 5.95 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.570 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.620 ------------------------------------------------------------------------------- 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= 0.136 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 : 2.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), 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 TRP 0.045 0.001 TRP F 216 HIS 0.003 0.000 HIS D 186 PHE 0.013 0.001 PHE G 9 TYR 0.007 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** 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 : 2.472 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: 1.5425 time to fit residues: 487.9083 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 : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.111249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.081935 restraints weight = 30166.620| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.39 r_work: 0.2910 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19748 Z= 0.209 Angle : 0.509 9.704 26714 Z= 0.273 Chirality : 0.043 0.163 3079 Planarity : 0.004 0.048 3404 Dihedral : 3.910 19.777 2690 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.57 % Allowed : 7.41 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2456 helix: 2.89 (0.18), residues: 898 sheet: 1.19 (0.22), residues: 544 loop : -0.51 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 PHE 0.015 0.001 PHE A 173 TYR 0.012 0.001 TYR B 136 ARG 0.003 0.000 ARG E 169 *********************** 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: 33 poor density : 221 time to evaluate : 2.358 Fit side-chains REVERT: A 150 ASP cc_start: 0.8420 (p0) cc_final: 0.8193 (p0) REVERT: A 179 ASN cc_start: 0.8094 (t0) cc_final: 0.7845 (t0) REVERT: B 151 ASP cc_start: 0.8404 (p0) cc_final: 0.8112 (p0) REVERT: D 207 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: E 203 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: F 171 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7270 (tp-100) REVERT: G 112 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8643 (p0) REVERT: J 40 ASN cc_start: 0.8707 (t0) cc_final: 0.8462 (t0) REVERT: M 121 GLU cc_start: 0.7962 (pm20) cc_final: 0.7606 (pm20) outliers start: 33 outliers final: 10 residues processed: 233 average time/residue: 1.5269 time to fit residues: 396.6967 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 : 2.565 ------------------------------------------------------------------------------- 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 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 112 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 63 THR 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 14 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 181 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN I 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.077809 restraints weight = 29269.495| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.48 r_work: 0.2808 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19748 Z= 0.219 Angle : 0.501 9.743 26714 Z= 0.270 Chirality : 0.043 0.172 3079 Planarity : 0.004 0.049 3404 Dihedral : 3.999 20.879 2690 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.42 % Allowed : 9.40 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2456 helix: 2.89 (0.18), residues: 897 sheet: 1.16 (0.22), residues: 542 loop : -0.53 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.010 0.001 TYR B 136 ARG 0.003 0.000 ARG E 164 *********************** 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 246 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.703 Fit side-chains REVERT: A 150 ASP cc_start: 0.8215 (p0) cc_final: 0.7958 (p0) REVERT: A 179 ASN cc_start: 0.7949 (t0) cc_final: 0.7672 (t0) REVERT: B 151 ASP cc_start: 0.8335 (p0) cc_final: 0.7987 (p0) REVERT: D 207 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: F 171 GLN cc_start: 0.7565 (tp-100) cc_final: 0.6940 (tp-100) REVERT: G 112 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8439 (p0) REVERT: G 130 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: I 40 GLN cc_start: 0.7661 (mm110) cc_final: 0.7384 (mm110) REVERT: K 128 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.5471 (mp10) REVERT: M 121 GLU cc_start: 0.7918 (pm20) cc_final: 0.7469 (pm20) outliers start: 30 outliers final: 13 residues processed: 227 average time/residue: 1.5692 time to fit residues: 395.5732 Evaluate side-chains 222 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 D residue 228 MET 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 I residue 60 VAL Chi-restraints excluded: chain J residue 55 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 202 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 183 optimal weight: 0.1980 chunk 226 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 J 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.076324 restraints weight = 29601.759| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.48 r_work: 0.2774 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19748 Z= 0.277 Angle : 0.535 9.538 26714 Z= 0.288 Chirality : 0.044 0.178 3079 Planarity : 0.005 0.051 3404 Dihedral : 4.182 23.112 2690 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.04 % Allowed : 10.64 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2456 helix: 2.77 (0.18), residues: 897 sheet: 1.14 (0.22), residues: 537 loop : -0.68 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.013 0.001 TYR B 136 ARG 0.003 0.000 ARG E 164 *********************** 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 252 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 2.626 Fit side-chains REVERT: A 150 ASP cc_start: 0.8303 (p0) cc_final: 0.8049 (p0) REVERT: A 179 ASN cc_start: 0.7891 (t0) cc_final: 0.7602 (t0) REVERT: B 151 ASP cc_start: 0.8441 (p0) cc_final: 0.8028 (p0) REVERT: C 23 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: D 207 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: E 186 GLU cc_start: 0.8115 (mp0) cc_final: 0.7634 (mt-10) REVERT: E 203 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: F 28 MET cc_start: 0.8704 (mtp) cc_final: 0.8391 (mtm) REVERT: F 171 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7021 (tp-100) REVERT: G 112 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8506 (p0) REVERT: G 130 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: I 43 ARG cc_start: 0.8302 (mtm110) cc_final: 0.8026 (mtm-85) REVERT: I 51 ARG cc_start: 0.6777 (ttt90) cc_final: 0.6477 (tpt170) REVERT: I 283 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: M 117 GLU cc_start: 0.7287 (tp30) cc_final: 0.6817 (mp0) REVERT: M 121 GLU cc_start: 0.7990 (pm20) cc_final: 0.7520 (pm20) outliers start: 43 outliers final: 17 residues processed: 234 average time/residue: 1.6533 time to fit residues: 429.3300 Evaluate side-chains 220 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 23 GLN 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 167 SER 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 130 GLU Chi-restraints excluded: chain G residue 234 GLU 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 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 81 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 K 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.078008 restraints weight = 29488.253| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.49 r_work: 0.2778 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19748 Z= 0.189 Angle : 0.488 9.685 26714 Z= 0.264 Chirality : 0.042 0.174 3079 Planarity : 0.004 0.052 3404 Dihedral : 4.028 21.332 2690 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.66 % Allowed : 12.11 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2456 helix: 2.87 (0.18), residues: 897 sheet: 1.18 (0.22), residues: 538 loop : -0.60 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.012 0.001 PHE A 173 TYR 0.010 0.001 TYR B 136 ARG 0.002 0.000 ARG E 164 *********************** 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 244 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.588 Fit side-chains REVERT: A 150 ASP cc_start: 0.8210 (p0) cc_final: 0.7900 (p0) REVERT: A 179 ASN cc_start: 0.7927 (t0) cc_final: 0.7654 (t0) REVERT: B 151 ASP cc_start: 0.8282 (p0) cc_final: 0.7927 (p0) REVERT: C 23 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: D 207 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: E 186 GLU cc_start: 0.8065 (mp0) cc_final: 0.7568 (mt-10) REVERT: E 203 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: F 28 MET cc_start: 0.8661 (mtp) cc_final: 0.8363 (mtm) REVERT: F 171 GLN cc_start: 0.7625 (tp-100) cc_final: 0.6943 (tp-100) REVERT: G 112 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8428 (p0) REVERT: G 130 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: I 43 ARG cc_start: 0.8318 (mtm110) cc_final: 0.8047 (mtm-85) REVERT: I 51 ARG cc_start: 0.6781 (ttt90) cc_final: 0.6470 (tpt170) REVERT: K 128 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5439 (mp10) REVERT: M 117 GLU cc_start: 0.7267 (tp30) cc_final: 0.6794 (mp0) REVERT: M 121 GLU cc_start: 0.8004 (pm20) cc_final: 0.7530 (pm20) outliers start: 35 outliers final: 19 residues processed: 227 average time/residue: 1.5850 time to fit residues: 399.6223 Evaluate side-chains 231 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 23 GLN 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 G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 144 THR 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 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 191 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 99 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 233 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 K 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081147 restraints weight = 30011.025| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.46 r_work: 0.2875 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19748 Z= 0.124 Angle : 0.442 10.040 26714 Z= 0.240 Chirality : 0.041 0.157 3079 Planarity : 0.004 0.051 3404 Dihedral : 3.741 17.830 2690 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.57 % Allowed : 12.77 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2456 helix: 3.02 (0.18), residues: 899 sheet: 1.26 (0.22), residues: 539 loop : -0.44 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.003 0.000 HIS E 65 PHE 0.012 0.001 PHE A 173 TYR 0.008 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** 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 258 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 2.407 Fit side-chains REVERT: A 150 ASP cc_start: 0.8203 (p0) cc_final: 0.7969 (p0) REVERT: A 179 ASN cc_start: 0.7967 (t0) cc_final: 0.7714 (t0) REVERT: B 151 ASP cc_start: 0.8128 (p0) cc_final: 0.7848 (p0) REVERT: C 23 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: D 166 ASP cc_start: 0.9068 (m-30) cc_final: 0.8839 (m-30) REVERT: D 207 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: E 186 GLU cc_start: 0.8053 (mp0) cc_final: 0.7545 (mt-10) REVERT: E 203 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: F 28 MET cc_start: 0.8623 (mtp) cc_final: 0.8287 (mtm) REVERT: F 94 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7559 (tt0) REVERT: F 171 GLN cc_start: 0.7566 (tp-100) cc_final: 0.6924 (tp-100) REVERT: I 51 ARG cc_start: 0.6802 (ttt90) cc_final: 0.6558 (tpt-90) REVERT: I 283 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: K 128 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5498 (mp10) REVERT: M 117 GLU cc_start: 0.7263 (tp30) cc_final: 0.6765 (mp0) REVERT: M 121 GLU cc_start: 0.8008 (pm20) cc_final: 0.7580 (pm20) outliers start: 33 outliers final: 16 residues processed: 245 average time/residue: 1.5411 time to fit residues: 426.1888 Evaluate side-chains 227 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 23 GLN 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 183 GLU 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 G residue 90 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR 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 M residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 42 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 122 optimal weight: 0.0050 chunk 161 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 G 224 ASN I 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.077180 restraints weight = 29421.293| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.47 r_work: 0.2795 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.043 19748 Z= 0.253 Angle : 0.522 9.440 26714 Z= 0.280 Chirality : 0.043 0.172 3079 Planarity : 0.004 0.053 3404 Dihedral : 4.023 20.246 2690 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2456 helix: 2.86 (0.18), residues: 897 sheet: 1.22 (0.22), residues: 537 loop : -0.59 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.005 0.001 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.012 0.001 TYR B 136 ARG 0.003 0.000 ARG I 43 *********************** 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 237 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 2.564 Fit side-chains REVERT: A 150 ASP cc_start: 0.8296 (p0) cc_final: 0.8021 (p0) REVERT: A 179 ASN cc_start: 0.7920 (t0) cc_final: 0.7643 (t0) REVERT: B 151 ASP cc_start: 0.8227 (p0) cc_final: 0.7860 (p0) REVERT: C 23 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: D 207 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: E 186 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: E 203 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: F 28 MET cc_start: 0.8639 (mtp) cc_final: 0.8337 (mtm) REVERT: F 94 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7605 (tt0) REVERT: F 171 GLN cc_start: 0.7646 (tp-100) cc_final: 0.6994 (tp-100) REVERT: I 43 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: I 283 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: K 128 GLN cc_start: 0.6423 (OUTLIER) cc_final: 0.5487 (mp10) REVERT: M 117 GLU cc_start: 0.7297 (tp30) cc_final: 0.6738 (mp0) REVERT: M 121 GLU cc_start: 0.8006 (pm20) cc_final: 0.7597 (pm20) outliers start: 35 outliers final: 21 residues processed: 221 average time/residue: 1.5478 time to fit residues: 380.8344 Evaluate side-chains 220 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 23 GLN 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 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 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 J residue 144 THR Chi-restraints excluded: chain J residue 226 GLU 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 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 83 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 232 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 108 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 I 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.080590 restraints weight = 29411.952| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.49 r_work: 0.2828 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19748 Z= 0.131 Angle : 0.450 9.805 26714 Z= 0.244 Chirality : 0.041 0.165 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.756 17.915 2690 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.52 % Allowed : 13.53 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.17), residues: 2456 helix: 3.01 (0.18), residues: 898 sheet: 1.25 (0.22), residues: 541 loop : -0.45 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.003 0.000 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.008 0.001 TYR B 156 ARG 0.003 0.000 ARG I 43 *********************** 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: 32 poor density : 209 time to evaluate : 1.947 Fit side-chains REVERT: A 150 ASP cc_start: 0.8134 (p0) cc_final: 0.7827 (p0) REVERT: A 179 ASN cc_start: 0.7863 (t0) cc_final: 0.7603 (t0) REVERT: B 151 ASP cc_start: 0.8031 (p0) cc_final: 0.7764 (p0) REVERT: C 23 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: D 65 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7314 (pp20) REVERT: D 166 ASP cc_start: 0.9016 (m-30) cc_final: 0.8793 (m-30) REVERT: D 207 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: E 4 ASN cc_start: 0.8272 (t0) cc_final: 0.7678 (m110) REVERT: E 186 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: E 203 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: F 28 MET cc_start: 0.8580 (mtp) cc_final: 0.8234 (mtm) REVERT: F 171 GLN cc_start: 0.7542 (tp-100) cc_final: 0.6908 (tp-100) REVERT: H 110 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: I 43 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: I 283 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: J 161 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: K 127 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7780 (ttmt) REVERT: K 128 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5526 (mp10) REVERT: M 117 GLU cc_start: 0.7295 (tp30) cc_final: 0.6718 (mp0) REVERT: M 121 GLU cc_start: 0.8032 (pm20) cc_final: 0.7593 (pm20) outliers start: 32 outliers final: 16 residues processed: 226 average time/residue: 1.5341 time to fit residues: 386.1504 Evaluate side-chains 225 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLN 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 183 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU 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 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 93 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 161 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 157 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 F 64 ASN G 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.077955 restraints weight = 29230.985| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.48 r_work: 0.2809 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19748 Z= 0.218 Angle : 0.507 9.400 26714 Z= 0.272 Chirality : 0.042 0.165 3079 Planarity : 0.004 0.053 3404 Dihedral : 3.941 19.106 2690 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.52 % Allowed : 13.96 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2456 helix: 2.91 (0.18), residues: 897 sheet: 1.26 (0.22), residues: 537 loop : -0.54 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.011 0.001 TYR B 136 ARG 0.003 0.000 ARG I 43 *********************** 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 232 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.545 Fit side-chains REVERT: A 150 ASP cc_start: 0.8268 (p0) cc_final: 0.7989 (p0) REVERT: A 179 ASN cc_start: 0.7935 (t0) cc_final: 0.7709 (t0) REVERT: B 151 ASP cc_start: 0.8137 (p0) cc_final: 0.7773 (p0) REVERT: C 23 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: D 10 ARG cc_start: 0.8592 (mtt180) cc_final: 0.7688 (mtm110) REVERT: D 65 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7316 (pp20) REVERT: D 166 ASP cc_start: 0.9065 (m-30) cc_final: 0.8831 (m-30) REVERT: D 207 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: E 186 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: E 203 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7233 (mt0) REVERT: F 28 MET cc_start: 0.8627 (mtp) cc_final: 0.8331 (mtm) REVERT: F 94 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7558 (tt0) REVERT: F 171 GLN cc_start: 0.7619 (tp-100) cc_final: 0.6971 (tp-100) REVERT: H 110 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: I 43 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: I 283 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: J 161 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: M 117 GLU cc_start: 0.7290 (tp30) cc_final: 0.6753 (mp0) REVERT: M 121 GLU cc_start: 0.8008 (pm20) cc_final: 0.7595 (pm20) outliers start: 32 outliers final: 18 residues processed: 220 average time/residue: 1.4901 time to fit residues: 366.5929 Evaluate side-chains 222 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 23 GLN 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 10 VAL Chi-restraints excluded: chain E residue 186 GLU 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 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 93 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL 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 61 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 206 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 F 64 ASN G 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079933 restraints weight = 29405.054| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.48 r_work: 0.2807 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19748 Z= 0.150 Angle : 0.465 9.906 26714 Z= 0.251 Chirality : 0.041 0.157 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.798 18.024 2690 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 13.87 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2456 helix: 2.98 (0.18), residues: 898 sheet: 1.29 (0.22), residues: 538 loop : -0.47 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.003 0.001 HIS E 65 PHE 0.012 0.001 PHE A 173 TYR 0.008 0.001 TYR B 136 ARG 0.002 0.000 ARG I 43 ********************** 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 231 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 2.341 Fit side-chains REVERT: A 150 ASP cc_start: 0.8150 (p0) cc_final: 0.7830 (p0) REVERT: A 179 ASN cc_start: 0.7875 (t0) cc_final: 0.7652 (t0) REVERT: B 151 ASP cc_start: 0.7999 (p0) cc_final: 0.7713 (p0) REVERT: B 209 GLU cc_start: 0.7364 (pp20) cc_final: 0.7162 (pp20) REVERT: C 23 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: D 10 ARG cc_start: 0.8566 (mtt180) cc_final: 0.7624 (mtp180) REVERT: D 65 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7291 (pp20) REVERT: D 166 ASP cc_start: 0.9010 (m-30) cc_final: 0.8765 (m-30) REVERT: D 207 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: E 4 ASN cc_start: 0.8276 (t0) cc_final: 0.7676 (m110) REVERT: E 186 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: E 203 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: F 28 MET cc_start: 0.8575 (mtp) cc_final: 0.8228 (mtm) REVERT: F 94 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7526 (tt0) REVERT: F 171 GLN cc_start: 0.7535 (tp-100) cc_final: 0.6868 (tp-100) REVERT: G 146 GLU cc_start: 0.8314 (pt0) cc_final: 0.8067 (pm20) REVERT: H 110 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: I 43 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8071 (mtm-85) REVERT: I 283 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: J 161 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: K 128 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.5466 (mp10) REVERT: M 117 GLU cc_start: 0.7285 (tp30) cc_final: 0.6748 (mp0) REVERT: M 121 GLU cc_start: 0.8018 (pm20) cc_final: 0.7563 (pm20) outliers start: 29 outliers final: 18 residues processed: 218 average time/residue: 1.5349 time to fit residues: 372.5661 Evaluate side-chains 226 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLN 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 E residue 10 VAL 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 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 J residue 144 THR Chi-restraints excluded: chain J residue 161 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 210 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 161 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 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 = 0.3419 r_free = 0.3419 target = 0.111007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080879 restraints weight = 29548.177| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.49 r_work: 0.2852 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19748 Z= 0.138 Angle : 0.459 9.586 26714 Z= 0.247 Chirality : 0.041 0.152 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.697 16.967 2690 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.33 % Allowed : 14.10 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.17), residues: 2456 helix: 3.02 (0.18), residues: 899 sheet: 1.28 (0.22), residues: 540 loop : -0.42 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 122 HIS 0.003 0.000 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.008 0.001 TYR B 136 ARG 0.002 0.000 ARG I 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14737.25 seconds wall clock time: 263 minutes 3.17 seconds (15783.17 seconds total)