Starting phenix.real_space_refine on Tue Nov 18 05:30:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dne_47038/11_2025/9dne_47038.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.078 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 43 5.16 5 C 7562 2.51 5 N 1947 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1238 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 25, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1247 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 25, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1263 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 26, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 148 Chain: "B" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1276 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 192} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 165 Chain: "E" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1271 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 24, 'ASN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 167 Chain: "F" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1306 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 192} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 26, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "G" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1275 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 25, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 176 Chain: "H" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1280 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 26, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 150 Chain: "I" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1280 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 192} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 163 Time building chain proxies: 3.41, per 1000 atoms: 0.30 Number of scatterers: 11436 At special positions: 0 Unit cell: (160.17, 183.774, 109.59, 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 43 16.00 O 1884 8.00 N 1947 7.00 C 7562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 223 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 203 " distance=2.04 Simple disulfide: pdb=" SG CYS E 165 " - pdb=" SG CYS E 203 " distance=2.02 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 203 " distance=2.04 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 185 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS I 165 " - pdb=" SG CYS I 203 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 624.6 milliseconds 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 30 sheets defined 55.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.661A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 76 through 82 removed outlier: 3.730A pdb=" N GLU D 80 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 157 through 165 removed outlier: 4.206A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.629A pdb=" N VAL C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.744A pdb=" N ARG C 60 " --> pdb=" O MET C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.633A pdb=" N GLN C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 132 through 137 removed outlier: 4.037A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 4.266A pdb=" N VAL C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.690A pdb=" N GLU C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.232A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.764A pdb=" N GLU A 80 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.878A pdb=" N LYS A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 4.125A pdb=" N VAL A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 4.275A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.762A pdb=" N ALA A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.665A pdb=" N GLU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 95 through 103 removed outlier: 5.464A pdb=" N LYS B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 removed outlier: 4.491A pdb=" N LYS B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 137 through 144 removed outlier: 4.027A pdb=" N VAL B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.011A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 4.295A pdb=" N VAL E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 171 Processing helix chain 'E' and resid 185 through 204 removed outlier: 4.701A pdb=" N GLU E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 20 through 34 Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.680A pdb=" N GLU F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 95 through 104 removed outlier: 5.462A pdb=" N LYS F 101 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 removed outlier: 4.590A pdb=" N LYS F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS F 122 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 137 through 144 removed outlier: 4.215A pdb=" N VAL F 141 " --> pdb=" O GLY F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 185 through 201 Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 113 through 122 Processing helix chain 'G' and resid 132 through 137 removed outlier: 4.091A pdb=" N VAL G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 4.268A pdb=" N VAL G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY G 146 " --> pdb=" O GLU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 171 Processing helix chain 'G' and resid 185 through 204 removed outlier: 3.735A pdb=" N GLU G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 31 removed outlier: 4.248A pdb=" N GLU H 25 " --> pdb=" O ARG H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 76 through 82 removed outlier: 3.714A pdb=" N GLU H 80 " --> pdb=" O PHE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 133 through 140 Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.105A pdb=" N VAL H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 164 removed outlier: 4.208A pdb=" N VAL H 161 " --> pdb=" O GLY H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 191 Processing helix chain 'H' and resid 205 through 221 Processing helix chain 'I' and resid 3 through 11 Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.988A pdb=" N LYS I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 55 through 60' Processing helix chain 'I' and resid 72 through 82 Processing helix chain 'I' and resid 95 through 103 removed outlier: 5.586A pdb=" N LYS I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 121 removed outlier: 4.360A pdb=" N LYS I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 137 Processing helix chain 'I' and resid 137 through 145 removed outlier: 4.055A pdb=" N VAL I 141 " --> pdb=" O GLY I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 171 Processing helix chain 'I' and resid 178 through 181 Processing helix chain 'I' and resid 185 through 201 Processing sheet with id=AA1, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.763A pdb=" N ILE D 59 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE D 32 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU D 60 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 34 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 33 " --> pdb=" O VAL D 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 106 through 108 removed outlier: 6.744A pdb=" N ILE D 107 " --> pdb=" O MET D 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 42 Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 87 removed outlier: 4.421A pdb=" N LEU A 58 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 33 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 108 removed outlier: 6.744A pdb=" N ILE A 107 " --> pdb=" O MET A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.628A pdb=" N LEU A 148 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.471A pdb=" N LEU B 38 " --> pdb=" O ILE B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB5, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'E' and resid 38 through 42 Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AB8, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AB9, first strand: chain 'F' and resid 64 through 68 removed outlier: 6.751A pdb=" N ILE F 39 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY F 68 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE F 41 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 12 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU F 40 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA F 14 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR F 42 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU F 16 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 86 through 88 Processing sheet with id=AC2, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AC3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC4, first strand: chain 'G' and resid 38 through 42 Processing sheet with id=AC5, first strand: chain 'G' and resid 86 through 88 Processing sheet with id=AC6, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'H' and resid 84 through 87 removed outlier: 6.881A pdb=" N ILE H 32 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU H 60 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA H 34 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 33 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'H' and resid 130 through 131 removed outlier: 6.745A pdb=" N LEU H 148 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 64 through 68 removed outlier: 6.996A pdb=" N ILE I 12 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU I 40 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA I 14 " --> pdb=" O GLU I 40 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR I 42 " --> pdb=" O ALA I 14 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU I 16 " --> pdb=" O THR I 42 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 86 through 88 Processing sheet with id=AD3, first strand: chain 'I' and resid 110 through 111 650 hydrogen bonds defined for protein. 1860 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: 1.86 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2763 1.33 - 1.46: 3457 1.46 - 1.59: 5406 1.59 - 1.72: 0 1.72 - 1.85: 68 Bond restraints: 11694 Sorted by residual: bond pdb=" CA LYS I 129 " pdb=" CB LYS I 129 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.34e-02 5.57e+03 1.02e+01 bond pdb=" C LYS I 129 " pdb=" O LYS I 129 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.22e-02 6.72e+03 9.48e+00 bond pdb=" CA LYS I 129 " pdb=" C LYS I 129 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.23e-02 6.61e+03 7.28e+00 bond pdb=" C PHE I 90 " pdb=" O PHE I 90 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.39e-02 5.18e+03 7.13e+00 bond pdb=" CA LYS B 129 " pdb=" CB LYS B 129 " ideal model delta sigma weight residual 1.529 1.496 0.032 1.34e-02 5.57e+03 5.85e+00 ... (remaining 11689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 14590 1.81 - 3.61: 1265 3.61 - 5.42: 157 5.42 - 7.23: 117 7.23 - 9.03: 25 Bond angle restraints: 16154 Sorted by residual: angle pdb=" C GLY D 157 " pdb=" N PRO D 158 " pdb=" CA PRO D 158 " ideal model delta sigma weight residual 119.56 128.59 -9.03 1.02e+00 9.61e-01 7.85e+01 angle pdb=" C GLY E 137 " pdb=" N PRO E 138 " pdb=" CA PRO E 138 " ideal model delta sigma weight residual 119.56 128.18 -8.62 1.02e+00 9.61e-01 7.14e+01 angle pdb=" C GLY G 137 " pdb=" N PRO G 138 " pdb=" CA PRO G 138 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 angle pdb=" C GLY A 157 " pdb=" N PRO A 158 " pdb=" CA PRO A 158 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" C GLY H 157 " pdb=" N PRO H 158 " pdb=" CA PRO H 158 " ideal model delta sigma weight residual 119.56 127.98 -8.42 1.02e+00 9.61e-01 6.82e+01 ... (remaining 16149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6439 17.47 - 34.94: 132 34.94 - 52.40: 24 52.40 - 69.87: 2 69.87 - 87.34: 4 Dihedral angle restraints: 6601 sinusoidal: 1459 harmonic: 5142 Sorted by residual: dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 203 " pdb=" CB CYS B 203 " ideal model delta sinusoidal sigma weight residual -86.00 -173.34 87.34 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS F 165 " pdb=" SG CYS F 165 " pdb=" SG CYS F 203 " pdb=" CB CYS F 203 " ideal model delta sinusoidal sigma weight residual 93.00 177.92 -84.92 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS I 165 " pdb=" SG CYS I 165 " pdb=" SG CYS I 203 " pdb=" CB CYS I 203 " ideal model delta sinusoidal sigma weight residual 93.00 166.84 -73.84 1 1.00e+01 1.00e-02 6.93e+01 ... (remaining 6598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1377 0.051 - 0.103: 518 0.103 - 0.154: 155 0.154 - 0.206: 28 0.206 - 0.257: 3 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CA THR D 135 " pdb=" N THR D 135 " pdb=" C THR D 135 " pdb=" CB THR D 135 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA VAL H 65 " pdb=" N VAL H 65 " pdb=" C VAL H 65 " pdb=" CB VAL H 65 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU C 16 " pdb=" CB LEU C 16 " pdb=" CD1 LEU C 16 " pdb=" CD2 LEU C 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2078 not shown) Planarity restraints: 2091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 128 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C LEU I 128 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU I 128 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS I 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 135 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C THR D 135 " 0.030 2.00e-02 2.50e+03 pdb=" O THR D 135 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU D 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 152 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C PRO D 152 " 0.028 2.00e-02 2.50e+03 pdb=" O PRO D 152 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 153 " -0.009 2.00e-02 2.50e+03 ... (remaining 2088 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 5452 2.95 - 3.44: 11383 3.44 - 3.93: 18171 3.93 - 4.41: 20955 4.41 - 4.90: 33071 Nonbonded interactions: 89032 Sorted by model distance: nonbonded pdb=" CE LYS B 129 " pdb=" OG1 THR B 156 " model vdw 2.467 3.440 nonbonded pdb=" O MET D 141 " pdb=" N GLY D 144 " model vdw 2.529 3.120 nonbonded pdb=" N THR H 64 " pdb=" N VAL H 65 " model vdw 2.531 2.560 nonbonded pdb=" N MET E 57 " pdb=" N LEU E 58 " model vdw 2.535 2.560 nonbonded pdb=" N THR G 44 " pdb=" N VAL G 45 " model vdw 2.538 2.560 ... (remaining 89027 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 22 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 44 or resid 48 through \ 52 or resid 54 through 57 or (resid 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 60 or (resid 61 through 62 and (name N or n \ ame CA or name C or name O or name CB )) or resid 63 through 69 or resid 71 thro \ ugh 73 or (resid 75 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 79 or (resid 82 through 85 and (name N or name CA or name C or \ name O or name CB )) or (resid 86 through 102 and (name N or name CA or name C o \ r name O or name CB )) or resid 103 through 109 or resid 111 or (resid 112 throu \ gh 118 and (name N or name CA or name C or name O or name CB )) or resid 119 thr \ ough 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) \ or resid 126 through 127 or (resid 128 and (name N or name CA or name C or name \ O or name CB )) or resid 129 through 131 or (resid 132 through 133 and (name N o \ r name CA or name C or name O or name CB )) or resid 134 or (resid 135 through 1 \ 37 and (name N or name CA or name C or name O or name CB )) or (resid 139 throug \ h 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thro \ ugh 150 or resid 152 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )) or resid 156 through 158 or (resid 159 and (name N or na \ me CA or name C or name O or name CB )) or resid 160 through 175 or (resid 176 a \ nd (name N or name CA or name C or name O or name CB )) or resid 177 through 178 \ or (resid 179 through 184 and (name N or name CA or name C or name O or name CB \ )) or resid 185 through 192 or (resid 193 through 195 and (name N or name CA or \ name C or name O or name CB )) or resid 196 through 204 or resid 206 or resid 2 \ 08 through 211 or resid 213 or resid 216 through 217 or resid 219 through 220 or \ resid 222 through 223)) selection = (chain 'B' and (resid 2 through 14 or (resid 15 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 24 or (resid 28 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 32 or resid 34 through 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 40 or (resid 41 through 42 and (name N or \ name CA or name C or name O or name CB )) or resid 43 through 49 or (resid 51 th \ rough 53 and (name N or name CA or name C or name O or name CB )) or resid 55 or \ resid 58 through 59 or (resid 62 through 65 and (name N or name CA or name C or \ name O or name CB )) or (resid 66 through 82 and (name N or name CA or name C o \ r name O or name CB )) or resid 83 through 89 or resid 91 or (resid 92 through 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 through 1 \ 04 or (resid 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 through 107 or (resid 108 and (name N or name CA or name C or name O or n \ ame CB )) or resid 109 through 111 or (resid 112 through 113 and (name N or name \ CA or name C or name O or name CB )) or resid 114 or (resid 115 through 117 and \ (name N or name CA or name C or name O or name CB )) or (resid 119 through 123 \ and (name N or name CA or name C or name O or name CB )) or resid 124 through 13 \ 0 or resid 132 through 134 or (resid 135 and (name N or name CA or name C or nam \ e O or name CB )) or resid 136 through 143 or (resid 144 through 145 and (name N \ or name CA or name C or name O or name CB )) or resid 146 through 155 or (resid \ 156 and (name N or name CA or name C or name O or name CB )) or resid 157 throu \ gh 158 or (resid 159 through 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 174 or (resid 175 and (name N or name CA or name \ C or name O or name CB )) or resid 176 or (resid 177 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 178 through 183 and (name N or name CA o \ r name C or name O or name CB )) or resid 184 or resid 186 or resid 188 through \ 191 or resid 193 or resid 196 or (resid 197 and (name N or name CA or name C or \ name O or name CB )) or (resid 199 through 200 and (name N or name CA or name C \ or name O or name CB )) or resid 202 through 203)) selection = (chain 'C' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 14 or (resid 15 through 20 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 24 or (resid 28 through 3 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 31 through 3 \ 2 or resid 34 through 35 or (resid 36 and (name N or name CA or name C or name O \ or name CB )) or resid 37 or (resid 38 and (name N or name CA or name C or name \ O or name CB )) or resid 39 through 40 or (resid 41 through 42 and (name N or n \ ame CA or name C or name O or name CB )) or resid 43 through 44 or (resid 45 and \ (name N or name CA or name C or name O or name CB )) or resid 46 through 49 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) or \ (resid 55 and (name N or name CA or name C or name O or name CB )) or resid 58 \ through 59 or (resid 62 through 65 and (name N or name CA or name C or name O or \ name CB )) or (resid 66 through 82 and (name N or name CA or name C or name O o \ r name CB )) or resid 83 through 89 or resid 91 or (resid 92 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 104 or (res \ id 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 117 or resid 119 through 130 or resid 132 through 134 or (resid 135 and (na \ me N or name CA or name C or name O or name CB )) or resid 136 through 158 or (r \ esid 159 through 164 and (name N or name CA or name C or name O or name CB )) or \ resid 165 through 172 or (resid 173 through 175 and (name N or name CA or name \ C or name O or name CB )) or resid 176 or (resid 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 through 184 or resid 186 or (resid 18 \ 8 through 191 and (name N or name CA or name C or name O or name CB )) or resid \ 193 or resid 196 or (resid 197 and (name N or name CA or name C or name O or nam \ e CB )) or resid 199 through 200 or resid 202 through 203)) selection = (chain 'D' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 40 or resid 42 through 44 or resid \ 48 through 52 or resid 54 through 57 or (resid 58 and (name N or name CA or nam \ e C or name O or name CB )) or resid 59 through 69 or resid 71 through 73 or res \ id 75 or resid 78 through 79 or resid 82 through 109 or resid 111 through 127 or \ (resid 128 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 9 through 131 or (resid 132 through 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 135 or (resid 136 through 137 and (name N \ or name CA or name C or name O or name CB )) or (resid 139 through 143 and (name \ N or name CA or name C or name O or name CB )) or resid 144 through 145 or (res \ id 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thr \ ough 150 or resid 152 through 158 or (resid 159 and (name N or name CA or name C \ or name O or name CB )) or resid 160 through 178 or (resid 179 through 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 192 or \ (resid 193 through 195 and (name N or name CA or name C or name O or name CB )) \ or (resid 196 through 203 and (name N or name CA or name C or name O or name CB \ )) or resid 204 or resid 206 or resid 208 through 211 or resid 213 or resid 216 \ through 217 or (resid 219 through 220 and (name N or name CA or name C or name \ O or name CB )) or resid 222 through 223)) selection = (chain 'E' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 14 or (resid 15 through 20 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 24 or (resid 28 through 3 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 31 through 3 \ 2 or resid 34 through 35 or (resid 36 and (name N or name CA or name C or name O \ or name CB )) or resid 37 through 40 or (resid 41 through 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 44 or (resid 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 49 or (r \ esid 51 through 53 and (name N or name CA or name C or name O or name CB )) or ( \ resid 55 and (name N or name CA or name C or name O or name CB )) or resid 58 th \ rough 59 or (resid 62 through 65 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 66 through 82 and (name N or name CA or name C or name O or \ name CB )) or (resid 83 through 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 through 89 or resid 91 or (resid 92 through 98 and (name \ N or name CA or name C or name O or name CB )) or resid 99 through 104 or (resi \ d 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thro \ ugh 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 or (resid 115 through 117 and (name N or \ name CA or name C or name O or name CB )) or (resid 119 through 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 130 or resid \ 132 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 163 or (resid 164 and (name N or name CA or name C o \ r name O or name CB )) or resid 165 through 172 or (resid 173 through 175 and (n \ ame N or name CA or name C or name O or name CB )) or resid 176 or (resid 177 an \ d (name N or name CA or name C or name O or name CB )) or (resid 178 through 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 or resid \ 186 or (resid 188 through 191 and (name N or name CA or name C or name O or name \ CB )) or resid 193 or resid 196 or (resid 197 and (name N or name CA or name C \ or name O or name CB )) or (resid 199 through 200 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 203)) selection = (chain 'F' and (resid 2 through 14 or (resid 15 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 24 or (resid 28 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 32 or resid 34 through 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 40 or (resid 41 through 42 and (name N or \ name CA or name C or name O or name CB )) or resid 43 or (resid 44 through 45 an \ d (name N or name CA or name C or name O or name CB )) or resid 46 through 49 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) o \ r (resid 55 and (name N or name CA or name C or name O or name CB )) or resid 58 \ through 59 or (resid 62 through 65 and (name N or name CA or name C or name O o \ r name CB )) or (resid 66 through 82 and (name N or name CA or name C or name O \ or name CB )) or (resid 83 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 through 89 or resid 91 or (resid 92 through 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 104 or (r \ esid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 t \ hrough 107 or (resid 108 and (name N or name CA or name C or name O or name CB ) \ ) or resid 109 through 111 or (resid 112 through 113 and (name N or name CA or n \ ame C or name O or name CB )) or resid 114 or (resid 115 through 117 and (name N \ or name CA or name C or name O or name CB )) or (resid 119 through 123 and (nam \ e N or name CA or name C or name O or name CB )) or resid 124 through 125 or (re \ sid 126 and (name N or name CA or name C or name O or name CB )) or resid 127 th \ rough 130 or resid 132 through 134 or (resid 135 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 138 or (resid 139 and (name N or \ name CA or name C or name O or name CB )) or resid 140 through 143 or (resid 144 \ through 145 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 46 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 158 or (resid 159 through 164 and (name N or name CA \ or name C or name O or name CB )) or resid 165 through 174 or (resid 175 and (na \ me N or name CA or name C or name O or name CB )) or resid 176 or (resid 177 and \ (name N or name CA or name C or name O or name CB )) or (resid 178 through 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 or resid 1 \ 86 or (resid 188 through 191 and (name N or name CA or name C or name O or name \ CB )) or resid 193 or resid 196 or (resid 197 and (name N or name CA or name C o \ r name O or name CB )) or (resid 199 through 200 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 203)) selection = (chain 'G' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 14 or (resid 15 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resid \ 28 through 30 and (name N or name CA or name C or name O or name CB )) or resid \ 31 through 32 or resid 34 through 35 or (resid 36 and (name N or name CA or nam \ e C or name O or name CB )) or resid 37 or (resid 38 and (name N or name CA or n \ ame C or name O or name CB )) or resid 39 through 40 or (resid 41 through 42 and \ (name N or name CA or name C or name O or name CB )) or resid 43 through 44 or \ (resid 45 and (name N or name CA or name C or name O or name CB )) or resid 46 t \ hrough 49 or (resid 51 through 53 and (name N or name CA or name C or name O or \ name CB )) or (resid 55 and (name N or name CA or name C or name O or name CB )) \ or resid 58 through 59 or (resid 62 through 65 and (name N or name CA or name C \ or name O or name CB )) or (resid 66 through 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 89 or resid 91 or (resid 92 throug \ h 98 and (name N or name CA or name C or name O or name CB )) or resid 99 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 107 or (resid 108 and (name N or name CA or name C or name O o \ r name CB )) or resid 109 through 111 or (resid 112 through 113 and (name N or n \ ame CA or name C or name O or name CB )) or resid 114 or (resid 115 through 117 \ and (name N or name CA or name C or name O or name CB )) or (resid 119 through 1 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 124 through \ 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or r \ esid 127 through 130 or resid 132 through 134 or (resid 135 and (name N or name \ CA or name C or name O or name CB )) or resid 136 through 158 or (resid 159 thro \ ugh 164 and (name N or name CA or name C or name O or name CB )) or resid 165 th \ rough 172 or (resid 173 through 175 and (name N or name CA or name C or name O o \ r name CB )) or resid 176 or (resid 177 and (name N or name CA or name C or name \ O or name CB )) or (resid 178 through 183 and (name N or name CA or name C or n \ ame O or name CB )) or resid 184 or resid 186 or (resid 188 through 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 193 or resid 196 or (r \ esid 197 and (name N or name CA or name C or name O or name CB )) or (resid 199 \ through 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 2 through 203)) selection = (chain 'H' and ((resid 22 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 44 or (resid 48 throug \ h 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throug \ h 52 or resid 54 through 55 or (resid 56 and (name N or name CA or name C or nam \ e O or name CB )) or resid 57 or (resid 58 and (name N or name CA or name C or n \ ame O or name CB )) or resid 59 through 60 or (resid 61 through 62 and (name N o \ r name CA or name C or name O or name CB )) or resid 63 through 64 or (resid 65 \ and (name N or name CA or name C or name O or name CB )) or resid 66 through 69 \ or (resid 71 through 73 and (name N or name CA or name C or name O or name CB )) \ or (resid 75 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 79 or (resid 82 through 85 and (name N or name CA or name C or name O \ or name CB )) or (resid 86 through 102 and (name N or name CA or name C or name \ O or name CB )) or resid 103 through 109 or resid 111 or (resid 112 through 118 \ and (name N or name CA or name C or name O or name CB )) or resid 119 through 1 \ 24 or (resid 125 and (name N or name CA or name C or name O or name CB )) or res \ id 126 through 127 or (resid 128 and (name N or name CA or name C or name O or n \ ame CB )) or resid 129 through 131 or (resid 132 through 133 and (name N or name \ CA or name C or name O or name CB )) or resid 134 or (resid 135 through 137 and \ (name N or name CA or name C or name O or name CB )) or (resid 139 through 143 \ and (name N or name CA or name C or name O or name CB )) or resid 144 through 15 \ 0 or resid 152 through 154 or (resid 155 and (name N or name CA or name C or nam \ e O or name CB )) or resid 156 through 178 or (resid 179 through 184 and (name N \ or name CA or name C or name O or name CB )) or resid 185 through 192 or (resid \ 193 through 195 and (name N or name CA or name C or name O or name CB )) or res \ id 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) or \ (resid 198 through 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 or resid 206 or (resid 208 through 211 and (name N or name CA or n \ ame C or name O or name CB )) or resid 213 or resid 216 or (resid 217 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 220 or resid \ 222 through 223)) selection = (chain 'I' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 14 or (resid 15 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resid \ 28 through 30 and (name N or name CA or name C or name O or name CB )) or resid \ 31 through 32 or resid 34 through 35 or (resid 36 and (name N or name CA or nam \ e C or name O or name CB )) or resid 37 or (resid 38 and (name N or name CA or n \ ame C or name O or name CB )) or resid 39 through 40 or (resid 41 through 42 and \ (name N or name CA or name C or name O or name CB )) or resid 43 through 49 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) or \ (resid 55 and (name N or name CA or name C or name O or name CB )) or resid 58 \ through 59 or (resid 62 through 65 and (name N or name CA or name C or name O or \ name CB )) or (resid 66 through 82 and (name N or name CA or name C or name O o \ r name CB )) or resid 83 through 89 or resid 91 or (resid 92 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 104 or (res \ id 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) \ or resid 109 through 111 or (resid 112 through 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 or (resid 115 through 117 and (name N o \ r name CA or name C or name O or name CB )) or (resid 119 through 123 and (name \ N or name CA or name C or name O or name CB )) or resid 124 through 130 or resid \ 132 through 134 or (resid 135 and (name N or name CA or name C or name O or nam \ e CB )) or resid 136 through 158 or (resid 159 through 164 and (name N or name C \ A or name C or name O or name CB )) or resid 165 through 172 or (resid 173 throu \ gh 175 and (name N or name CA or name C or name O or name CB )) or resid 176 or \ (resid 177 and (name N or name CA or name C or name O or name CB )) or (resid 17 \ 8 through 183 and (name N or name CA or name C or name O or name CB )) or resid \ 184 or resid 186 or (resid 188 through 191 and (name N or name CA or name C or n \ ame O or name CB )) or resid 193 or resid 196 or (resid 197 and (name N or name \ CA or name C or name O or name CB )) or resid 199 through 200 or resid 202 throu \ gh 203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 35.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.170 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.007 0.045 11703 Z= 0.436 Angle : 1.250 9.035 16172 Z= 0.893 Chirality : 0.058 0.257 2081 Planarity : 0.004 0.021 2091 Dihedral : 7.723 68.913 3262 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.15 % Favored : 95.30 % Rotamer: Outliers : 0.13 % Allowed : 0.92 % Favored : 98.94 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1809 helix: -0.16 (0.15), residues: 954 sheet: 0.41 (0.28), residues: 354 loop : 0.39 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 195 TYR 0.011 0.003 TYR D 138 PHE 0.013 0.002 PHE I 153 TRP 0.013 0.005 TRP A 187 HIS 0.004 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00685 (11694) covalent geometry : angle 1.24782 (16154) SS BOND : bond 0.01294 ( 9) SS BOND : angle 2.42253 ( 18) hydrogen bonds : bond 0.19361 ( 650) hydrogen bonds : angle 6.92249 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8131 (mttt) cc_final: 0.7594 (mmtp) REVERT: D 193 LEU cc_start: 0.8542 (tp) cc_final: 0.8190 (tp) REVERT: A 32 ILE cc_start: 0.9113 (tt) cc_final: 0.8812 (mp) REVERT: A 75 LEU cc_start: 0.8345 (mt) cc_final: 0.8086 (mp) REVERT: A 147 ILE cc_start: 0.8763 (mt) cc_final: 0.8338 (mt) REVERT: A 148 LEU cc_start: 0.8727 (mt) cc_final: 0.8506 (mt) REVERT: E 41 ILE cc_start: 0.9284 (mt) cc_final: 0.9028 (mm) REVERT: E 129 LYS cc_start: 0.8730 (tttt) cc_final: 0.8463 (tttp) REVERT: E 181 LEU cc_start: 0.9138 (tp) cc_final: 0.8890 (tt) REVERT: F 46 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: F 144 MET cc_start: 0.8180 (mmm) cc_final: 0.7974 (mpp) REVERT: G 108 MET cc_start: 0.8171 (ttp) cc_final: 0.7594 (ptm) REVERT: H 78 LEU cc_start: 0.9268 (mt) cc_final: 0.9012 (tp) outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.0940 time to fit residues: 31.7122 Evaluate side-chains 117 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 90 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077435 restraints weight = 34234.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078944 restraints weight = 27041.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079980 restraints weight = 19804.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080577 restraints weight = 16589.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080781 restraints weight = 15021.866| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11703 Z= 0.160 Angle : 0.579 7.399 16172 Z= 0.305 Chirality : 0.047 0.163 2081 Planarity : 0.005 0.041 2091 Dihedral : 4.711 48.110 1837 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.51 % Allowed : 11.08 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1809 helix: 1.10 (0.17), residues: 963 sheet: 0.60 (0.31), residues: 294 loop : 0.53 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 195 TYR 0.013 0.002 TYR A 138 PHE 0.020 0.001 PHE F 7 TRP 0.017 0.002 TRP I 167 HIS 0.006 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00366 (11694) covalent geometry : angle 0.57161 (16154) SS BOND : bond 0.00966 ( 9) SS BOND : angle 2.80503 ( 18) hydrogen bonds : bond 0.03759 ( 650) hydrogen bonds : angle 4.78566 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: D 128 MET cc_start: 0.8018 (ttp) cc_final: 0.7283 (ptm) REVERT: D 193 LEU cc_start: 0.8786 (tp) cc_final: 0.8517 (tp) REVERT: D 201 LEU cc_start: 0.9110 (tt) cc_final: 0.8842 (tp) REVERT: A 32 ILE cc_start: 0.9575 (tt) cc_final: 0.9121 (mt) REVERT: A 75 LEU cc_start: 0.8659 (mt) cc_final: 0.8256 (mp) REVERT: E 117 LEU cc_start: 0.9605 (tt) cc_final: 0.9395 (tp) REVERT: F 144 MET cc_start: 0.8769 (mmm) cc_final: 0.7400 (mmm) REVERT: H 78 LEU cc_start: 0.9237 (mt) cc_final: 0.8988 (mt) outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.0819 time to fit residues: 19.7117 Evaluate side-chains 124 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 HIS H 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072565 restraints weight = 34995.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074310 restraints weight = 26063.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074836 restraints weight = 19105.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075226 restraints weight = 17579.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075286 restraints weight = 15382.530| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11703 Z= 0.182 Angle : 0.570 12.336 16172 Z= 0.296 Chirality : 0.047 0.193 2081 Planarity : 0.005 0.044 2091 Dihedral : 4.329 33.372 1835 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.30 % Allowed : 11.74 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1809 helix: 1.59 (0.17), residues: 930 sheet: 0.67 (0.28), residues: 342 loop : 0.12 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 195 TYR 0.011 0.001 TYR F 107 PHE 0.018 0.001 PHE E 168 TRP 0.016 0.002 TRP C 167 HIS 0.006 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00404 (11694) covalent geometry : angle 0.56393 (16154) SS BOND : bond 0.00357 ( 9) SS BOND : angle 2.56006 ( 18) hydrogen bonds : bond 0.03231 ( 650) hydrogen bonds : angle 4.37676 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.419 Fit side-chains REVERT: D 128 MET cc_start: 0.8068 (ttp) cc_final: 0.7202 (ptm) REVERT: D 201 LEU cc_start: 0.9234 (tt) cc_final: 0.8944 (tp) REVERT: A 32 ILE cc_start: 0.9661 (tt) cc_final: 0.9328 (mt) REVERT: A 75 LEU cc_start: 0.8753 (mt) cc_final: 0.8381 (mp) REVERT: A 128 MET cc_start: 0.8518 (mmm) cc_final: 0.8025 (mmm) REVERT: F 144 MET cc_start: 0.8740 (mmm) cc_final: 0.7790 (mmt) REVERT: F 181 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8555 (pt) REVERT: H 78 LEU cc_start: 0.9261 (mt) cc_final: 0.9032 (mt) REVERT: I 11 LYS cc_start: 0.8832 (mttt) cc_final: 0.8585 (mttm) outliers start: 25 outliers final: 17 residues processed: 128 average time/residue: 0.0846 time to fit residues: 17.1392 Evaluate side-chains 119 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 203 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072680 restraints weight = 34872.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073659 restraints weight = 25029.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074474 restraints weight = 20015.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074635 restraints weight = 17229.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.075832 restraints weight = 16216.395| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11703 Z= 0.124 Angle : 0.520 11.288 16172 Z= 0.263 Chirality : 0.046 0.161 2081 Planarity : 0.004 0.043 2091 Dihedral : 4.080 33.149 1835 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 3.30 % Allowed : 13.85 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.21), residues: 1809 helix: 1.66 (0.17), residues: 948 sheet: 0.62 (0.28), residues: 342 loop : 0.12 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 195 TYR 0.010 0.001 TYR A 138 PHE 0.012 0.001 PHE E 168 TRP 0.013 0.002 TRP E 167 HIS 0.004 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00286 (11694) covalent geometry : angle 0.51267 (16154) SS BOND : bond 0.00344 ( 9) SS BOND : angle 2.63147 ( 18) hydrogen bonds : bond 0.02424 ( 650) hydrogen bonds : angle 4.02211 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.450 Fit side-chains REVERT: D 128 MET cc_start: 0.8060 (ttp) cc_final: 0.7196 (ptm) REVERT: D 201 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8730 (tp) REVERT: A 32 ILE cc_start: 0.9585 (tt) cc_final: 0.9326 (mt) REVERT: A 75 LEU cc_start: 0.8598 (mt) cc_final: 0.8281 (mp) REVERT: A 128 MET cc_start: 0.8631 (mmm) cc_final: 0.8405 (mmm) REVERT: F 144 MET cc_start: 0.8824 (mmm) cc_final: 0.8181 (mmp) REVERT: F 145 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8001 (pttm) REVERT: F 181 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8414 (pt) REVERT: G 177 VAL cc_start: 0.9343 (t) cc_final: 0.9046 (m) outliers start: 25 outliers final: 15 residues processed: 135 average time/residue: 0.0864 time to fit residues: 18.5239 Evaluate side-chains 120 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 98 optimal weight: 0.0370 chunk 79 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073231 restraints weight = 34613.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074186 restraints weight = 24763.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074926 restraints weight = 20265.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075364 restraints weight = 17161.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075569 restraints weight = 15897.548| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11703 Z= 0.092 Angle : 0.511 11.035 16172 Z= 0.256 Chirality : 0.046 0.157 2081 Planarity : 0.004 0.044 2091 Dihedral : 3.987 32.720 1835 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 3.56 % Allowed : 14.38 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1809 helix: 1.70 (0.18), residues: 951 sheet: 0.63 (0.28), residues: 345 loop : 0.15 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 195 TYR 0.009 0.001 TYR A 138 PHE 0.014 0.001 PHE H 77 TRP 0.012 0.002 TRP E 167 HIS 0.002 0.000 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00204 (11694) covalent geometry : angle 0.50281 (16154) SS BOND : bond 0.00266 ( 9) SS BOND : angle 2.76146 ( 18) hydrogen bonds : bond 0.02285 ( 650) hydrogen bonds : angle 3.92677 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.452 Fit side-chains REVERT: D 128 MET cc_start: 0.8066 (ttp) cc_final: 0.7212 (ptm) REVERT: D 201 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 32 ILE cc_start: 0.9548 (tt) cc_final: 0.9326 (mt) REVERT: A 75 LEU cc_start: 0.8601 (mt) cc_final: 0.8275 (mp) REVERT: A 137 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8759 (mp) REVERT: F 29 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8450 (mm) REVERT: F 144 MET cc_start: 0.8829 (mmm) cc_final: 0.7804 (mmt) REVERT: F 145 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7962 (pttm) REVERT: F 181 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8368 (pt) REVERT: G 177 VAL cc_start: 0.9315 (t) cc_final: 0.9048 (m) outliers start: 27 outliers final: 14 residues processed: 130 average time/residue: 0.0880 time to fit residues: 17.8687 Evaluate side-chains 121 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068290 restraints weight = 35256.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069164 restraints weight = 27001.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070018 restraints weight = 21647.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.070139 restraints weight = 18549.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070322 restraints weight = 16930.600| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11703 Z= 0.214 Angle : 0.599 11.215 16172 Z= 0.308 Chirality : 0.048 0.181 2081 Planarity : 0.004 0.045 2091 Dihedral : 4.339 32.162 1835 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 3.83 % Allowed : 13.85 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.21), residues: 1809 helix: 1.57 (0.17), residues: 951 sheet: -0.23 (0.25), residues: 420 loop : 0.13 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 17 TYR 0.016 0.002 TYR A 138 PHE 0.013 0.002 PHE H 151 TRP 0.011 0.002 TRP D 187 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00494 (11694) covalent geometry : angle 0.59185 (16154) SS BOND : bond 0.00383 ( 9) SS BOND : angle 2.87655 ( 18) hydrogen bonds : bond 0.03391 ( 650) hydrogen bonds : angle 4.17751 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.325 Fit side-chains REVERT: A 137 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8991 (mt) REVERT: F 29 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8585 (mm) REVERT: F 117 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8987 (tp) REVERT: F 144 MET cc_start: 0.8892 (mmm) cc_final: 0.7986 (mmt) REVERT: F 145 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8110 (pttm) REVERT: F 181 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8291 (pt) outliers start: 29 outliers final: 22 residues processed: 123 average time/residue: 0.0799 time to fit residues: 15.8583 Evaluate side-chains 120 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 90 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 143 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.070181 restraints weight = 35141.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071014 restraints weight = 28347.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071856 restraints weight = 22321.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072282 restraints weight = 17598.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072476 restraints weight = 16209.082| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11703 Z= 0.114 Angle : 0.520 10.599 16172 Z= 0.261 Chirality : 0.046 0.166 2081 Planarity : 0.004 0.047 2091 Dihedral : 4.100 32.252 1835 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 15.04 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1809 helix: 1.71 (0.18), residues: 951 sheet: 0.33 (0.27), residues: 375 loop : -0.19 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 195 TYR 0.015 0.001 TYR A 138 PHE 0.010 0.001 PHE B 57 TRP 0.012 0.002 TRP E 167 HIS 0.003 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00264 (11694) covalent geometry : angle 0.51300 (16154) SS BOND : bond 0.00320 ( 9) SS BOND : angle 2.58723 ( 18) hydrogen bonds : bond 0.02528 ( 650) hydrogen bonds : angle 3.95579 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.396 Fit side-chains REVERT: A 137 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9020 (mt) REVERT: F 29 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8512 (mm) REVERT: F 144 MET cc_start: 0.8863 (mmm) cc_final: 0.7964 (mmt) REVERT: F 145 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8057 (pttm) REVERT: F 181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8185 (pt) outliers start: 29 outliers final: 21 residues processed: 124 average time/residue: 0.0826 time to fit residues: 16.3726 Evaluate side-chains 122 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069874 restraints weight = 34916.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071316 restraints weight = 25349.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071971 restraints weight = 18602.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072329 restraints weight = 16784.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.072414 restraints weight = 14900.229| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11703 Z= 0.112 Angle : 0.515 13.308 16172 Z= 0.256 Chirality : 0.046 0.159 2081 Planarity : 0.004 0.043 2091 Dihedral : 3.945 31.989 1835 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.43 % Allowed : 15.57 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1809 helix: 1.78 (0.18), residues: 951 sheet: 0.44 (0.27), residues: 345 loop : -0.15 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 195 TYR 0.031 0.002 TYR A 138 PHE 0.010 0.001 PHE E 168 TRP 0.013 0.002 TRP E 167 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00259 (11694) covalent geometry : angle 0.50949 (16154) SS BOND : bond 0.00242 ( 9) SS BOND : angle 2.31033 ( 18) hydrogen bonds : bond 0.02383 ( 650) hydrogen bonds : angle 3.90572 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.441 Fit side-chains REVERT: A 137 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8968 (mt) REVERT: F 29 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8492 (mm) REVERT: F 144 MET cc_start: 0.8850 (mmm) cc_final: 0.7960 (mmt) REVERT: F 181 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8150 (pt) outliers start: 26 outliers final: 21 residues processed: 119 average time/residue: 0.0822 time to fit residues: 15.6852 Evaluate side-chains 117 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 108 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.069964 restraints weight = 34837.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070688 restraints weight = 24954.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071108 restraints weight = 20006.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071401 restraints weight = 18888.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071569 restraints weight = 16971.063| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11703 Z= 0.119 Angle : 0.518 13.278 16172 Z= 0.257 Chirality : 0.046 0.163 2081 Planarity : 0.004 0.042 2091 Dihedral : 3.936 31.977 1835 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.17 % Allowed : 16.89 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1809 helix: 1.81 (0.18), residues: 951 sheet: 0.30 (0.27), residues: 375 loop : -0.23 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 195 TYR 0.028 0.002 TYR A 138 PHE 0.012 0.001 PHE C 32 TRP 0.011 0.002 TRP E 167 HIS 0.002 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00276 (11694) covalent geometry : angle 0.51258 (16154) SS BOND : bond 0.00238 ( 9) SS BOND : angle 2.26305 ( 18) hydrogen bonds : bond 0.02428 ( 650) hydrogen bonds : angle 3.89639 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.413 Fit side-chains REVERT: A 137 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8978 (mt) REVERT: F 29 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8519 (mm) REVERT: F 144 MET cc_start: 0.8841 (mmm) cc_final: 0.7980 (mmt) REVERT: F 181 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8058 (pt) outliers start: 24 outliers final: 21 residues processed: 114 average time/residue: 0.0810 time to fit residues: 14.9861 Evaluate side-chains 116 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 175 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 158 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 149 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070551 restraints weight = 34875.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072281 restraints weight = 26003.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073083 restraints weight = 18778.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073559 restraints weight = 16425.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073649 restraints weight = 15263.993| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11703 Z= 0.084 Angle : 0.492 12.323 16172 Z= 0.241 Chirality : 0.046 0.151 2081 Planarity : 0.004 0.040 2091 Dihedral : 3.787 32.042 1835 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 17.41 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1809 helix: 1.82 (0.18), residues: 954 sheet: 0.16 (0.27), residues: 396 loop : -0.03 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 195 TYR 0.028 0.001 TYR A 138 PHE 0.009 0.001 PHE B 57 TRP 0.015 0.002 TRP G 167 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00184 (11694) covalent geometry : angle 0.48812 (16154) SS BOND : bond 0.00216 ( 9) SS BOND : angle 1.89947 ( 18) hydrogen bonds : bond 0.02034 ( 650) hydrogen bonds : angle 3.79231 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.475 Fit side-chains REVERT: D 136 GLU cc_start: 0.8555 (pt0) cc_final: 0.8108 (tt0) REVERT: A 137 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9107 (mt) REVERT: F 29 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 144 MET cc_start: 0.8806 (mmm) cc_final: 0.7954 (mmt) REVERT: F 181 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8071 (pt) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.0815 time to fit residues: 14.3436 Evaluate side-chains 111 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069589 restraints weight = 35193.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070818 restraints weight = 27526.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071804 restraints weight = 20803.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.072022 restraints weight = 17076.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072179 restraints weight = 15728.603| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11703 Z= 0.122 Angle : 0.512 12.763 16172 Z= 0.253 Chirality : 0.046 0.159 2081 Planarity : 0.004 0.041 2091 Dihedral : 3.816 31.877 1835 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 2.90 % Allowed : 17.28 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1809 helix: 1.87 (0.18), residues: 954 sheet: 0.05 (0.27), residues: 396 loop : -0.05 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 195 TYR 0.023 0.001 TYR A 138 PHE 0.011 0.001 PHE C 32 TRP 0.011 0.002 TRP D 187 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00284 (11694) covalent geometry : angle 0.50714 (16154) SS BOND : bond 0.00309 ( 9) SS BOND : angle 2.08303 ( 18) hydrogen bonds : bond 0.02369 ( 650) hydrogen bonds : angle 3.83239 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.95 seconds wall clock time: 39 minutes 19.16 seconds (2359.16 seconds total)