Starting phenix.real_space_refine on Tue Jul 29 13:54:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dne_47038/07_2025/9dne_47038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dne_47038/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dne_47038/07_2025/9dne_47038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dne_47038/07_2025/9dne_47038.map" model { file = "/net/cci-nas-00/data/ceres_data/9dne_47038/07_2025/9dne_47038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dne_47038/07_2025/9dne_47038.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 25, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 25, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 26, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 4, 'GLU:plan': 27, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 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: {'GLN:plan1': 3, 'GLU:plan': 24, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 7} 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: {'GLN:plan1': 3, 'GLU:plan': 26, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 25, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 26, 'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4} 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: {'GLN:plan1': 4, 'GLU:plan': 27, 'ARG:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 163 Time building chain proxies: 12.53, per 1000 atoms: 1.10 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: 2.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.61 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: 3.49 Time building geometry restraints manager: 3.31 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: 1035.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.600 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1073.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 TRP 0.013 0.005 TRP A 187 HIS 0.004 0.001 HIS H 111 PHE 0.013 0.002 PHE I 153 TYR 0.011 0.003 TYR D 138 ARG 0.001 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.19361 ( 650) hydrogen bonds : angle 6.92249 ( 1860) SS BOND : bond 0.01294 ( 9) SS BOND : angle 2.42253 ( 18) covalent geometry : bond 0.00685 (11694) covalent geometry : angle 1.24782 (16154) *********************** 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 : 1.289 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: 0.1958 time to fit residues: 66.0517 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 : 1.196 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.4980 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.092720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077929 restraints weight = 34056.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079396 restraints weight = 26363.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080252 restraints weight = 19673.310| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 11703 Z= 0.158 Angle : 0.572 7.949 16172 Z= 0.299 Chirality : 0.047 0.156 2081 Planarity : 0.004 0.043 2091 Dihedral : 4.714 47.702 1837 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1809 helix: 1.13 (0.17), residues: 966 sheet: 0.66 (0.31), residues: 294 loop : 0.57 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 167 HIS 0.006 0.001 HIS H 111 PHE 0.019 0.001 PHE D 52 TYR 0.014 0.002 TYR A 138 ARG 0.005 0.001 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 650) hydrogen bonds : angle 4.76683 ( 1860) SS BOND : bond 0.00927 ( 9) SS BOND : angle 3.31677 ( 18) covalent geometry : bond 0.00355 (11694) covalent geometry : angle 0.56182 (16154) *********************** 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 155 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: D 128 MET cc_start: 0.8006 (ttp) cc_final: 0.7265 (ptm) REVERT: D 193 LEU cc_start: 0.8800 (tp) cc_final: 0.8524 (tp) REVERT: D 201 LEU cc_start: 0.9100 (tt) cc_final: 0.8829 (tp) REVERT: A 32 ILE cc_start: 0.9566 (tt) cc_final: 0.9101 (mt) REVERT: A 75 LEU cc_start: 0.8644 (mt) cc_final: 0.8239 (mp) REVERT: E 117 LEU cc_start: 0.9602 (tt) cc_final: 0.9388 (tp) REVERT: F 144 MET cc_start: 0.8747 (mmm) cc_final: 0.7352 (mmm) REVERT: H 78 LEU cc_start: 0.9231 (mt) cc_final: 0.8978 (mt) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.1817 time to fit residues: 43.0104 Evaluate side-chains 123 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 I residue 52 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.087723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073267 restraints weight = 34870.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074704 restraints weight = 26727.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075625 restraints weight = 20340.817| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11703 Z= 0.168 Angle : 0.562 12.125 16172 Z= 0.291 Chirality : 0.047 0.205 2081 Planarity : 0.005 0.045 2091 Dihedral : 4.323 33.140 1835 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.03 % Allowed : 12.53 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1809 helix: 1.58 (0.17), residues: 930 sheet: 0.72 (0.28), residues: 342 loop : 0.16 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 167 HIS 0.006 0.001 HIS H 111 PHE 0.015 0.001 PHE E 168 TYR 0.011 0.001 TYR F 107 ARG 0.004 0.001 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 650) hydrogen bonds : angle 4.37821 ( 1860) SS BOND : bond 0.01026 ( 9) SS BOND : angle 2.19584 ( 18) covalent geometry : bond 0.00379 (11694) covalent geometry : angle 0.55703 (16154) *********************** 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 133 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.233 Fit side-chains REVERT: D 128 MET cc_start: 0.8033 (ttp) cc_final: 0.7160 (ptm) REVERT: D 136 GLU cc_start: 0.8865 (pt0) cc_final: 0.8584 (pt0) REVERT: D 201 LEU cc_start: 0.9225 (tt) cc_final: 0.8974 (tp) REVERT: A 32 ILE cc_start: 0.9664 (tt) cc_final: 0.9331 (mt) REVERT: A 75 LEU cc_start: 0.8786 (mt) cc_final: 0.8408 (mp) REVERT: F 144 MET cc_start: 0.8742 (mmm) cc_final: 0.7795 (mmt) REVERT: F 181 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8438 (pt) REVERT: H 78 LEU cc_start: 0.9254 (mt) cc_final: 0.9033 (mt) REVERT: I 11 LYS cc_start: 0.8815 (mttt) cc_final: 0.8580 (mttm) outliers start: 23 outliers final: 15 residues processed: 128 average time/residue: 0.1780 time to fit residues: 35.9552 Evaluate side-chains 113 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071581 restraints weight = 34886.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072304 restraints weight = 24887.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072613 restraints weight = 20203.788| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11703 Z= 0.172 Angle : 0.559 11.931 16172 Z= 0.286 Chirality : 0.047 0.155 2081 Planarity : 0.005 0.047 2091 Dihedral : 4.292 33.149 1835 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % Rotamer: Outliers : 4.22 % Allowed : 13.06 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1809 helix: 1.53 (0.17), residues: 948 sheet: 0.15 (0.27), residues: 369 loop : 0.20 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 167 HIS 0.005 0.001 HIS H 111 PHE 0.015 0.001 PHE E 168 TYR 0.014 0.001 TYR A 138 ARG 0.003 0.001 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 650) hydrogen bonds : angle 4.18856 ( 1860) SS BOND : bond 0.00363 ( 9) SS BOND : angle 2.46717 ( 18) covalent geometry : bond 0.00405 (11694) covalent geometry : angle 0.55327 (16154) *********************** 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 144 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.372 Fit side-chains REVERT: D 128 MET cc_start: 0.8137 (ttp) cc_final: 0.7263 (ptm) REVERT: D 201 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 32 ILE cc_start: 0.9629 (tt) cc_final: 0.9321 (mt) REVERT: A 75 LEU cc_start: 0.8611 (mt) cc_final: 0.8283 (mp) REVERT: A 137 LEU cc_start: 0.9385 (mp) cc_final: 0.9169 (mt) REVERT: A 147 ILE cc_start: 0.9237 (mp) cc_final: 0.8958 (mp) REVERT: F 117 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8818 (tp) REVERT: F 144 MET cc_start: 0.8811 (mmm) cc_final: 0.8160 (mmp) REVERT: F 145 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8038 (pttm) REVERT: F 181 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8484 (pt) REVERT: F 199 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8493 (ttmt) REVERT: I 11 LYS cc_start: 0.8850 (mttt) cc_final: 0.8619 (mttm) outliers start: 32 outliers final: 21 residues processed: 136 average time/residue: 0.1812 time to fit residues: 38.9988 Evaluate side-chains 129 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain A residue 131 VAL 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 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 117 LEU 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 32 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.084668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070218 restraints weight = 34701.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071332 restraints weight = 25624.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072121 restraints weight = 20043.314| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11703 Z= 0.160 Angle : 0.559 12.518 16172 Z= 0.284 Chirality : 0.047 0.151 2081 Planarity : 0.004 0.047 2091 Dihedral : 4.262 32.725 1835 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 4.22 % Allowed : 13.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1809 helix: 1.60 (0.17), residues: 948 sheet: 0.31 (0.28), residues: 345 loop : -0.02 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 167 HIS 0.004 0.001 HIS H 111 PHE 0.016 0.001 PHE H 77 TYR 0.014 0.001 TYR A 138 ARG 0.003 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02797 ( 650) hydrogen bonds : angle 4.10335 ( 1860) SS BOND : bond 0.00299 ( 9) SS BOND : angle 2.80223 ( 18) covalent geometry : bond 0.00373 (11694) covalent geometry : angle 0.55162 (16154) *********************** 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 138 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.322 Fit side-chains REVERT: D 128 MET cc_start: 0.8121 (ttp) cc_final: 0.7295 (ptm) REVERT: D 201 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8842 (tp) REVERT: A 32 ILE cc_start: 0.9539 (tt) cc_final: 0.9323 (mt) REVERT: A 75 LEU cc_start: 0.8635 (mt) cc_final: 0.8285 (mp) REVERT: A 128 MET cc_start: 0.8783 (mmm) cc_final: 0.8459 (mmm) REVERT: A 137 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9016 (mt) REVERT: F 144 MET cc_start: 0.8864 (mmm) cc_final: 0.7916 (mmt) REVERT: F 145 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8089 (pttm) REVERT: F 181 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8485 (pt) REVERT: F 199 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8290 (ttmt) outliers start: 32 outliers final: 21 residues processed: 131 average time/residue: 0.1732 time to fit residues: 35.9244 Evaluate side-chains 123 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 58 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 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 145 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 32 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.083726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069862 restraints weight = 35433.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070893 restraints weight = 30203.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071709 restraints weight = 21809.916| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11703 Z= 0.146 Angle : 0.539 11.264 16172 Z= 0.275 Chirality : 0.047 0.147 2081 Planarity : 0.004 0.046 2091 Dihedral : 4.146 32.020 1835 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 4.09 % Allowed : 13.98 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1809 helix: 1.67 (0.18), residues: 951 sheet: 0.37 (0.27), residues: 345 loop : -0.21 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 167 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE H 77 TYR 0.028 0.002 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02667 ( 650) hydrogen bonds : angle 4.03170 ( 1860) SS BOND : bond 0.00446 ( 9) SS BOND : angle 2.58558 ( 18) covalent geometry : bond 0.00339 (11694) covalent geometry : angle 0.53269 (16154) *********************** 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 139 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.219 Fit side-chains REVERT: D 201 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8809 (tp) REVERT: A 128 MET cc_start: 0.8417 (mmm) cc_final: 0.8146 (mmm) REVERT: A 137 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9009 (mt) REVERT: F 117 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8927 (tp) REVERT: F 144 MET cc_start: 0.8866 (mmm) cc_final: 0.7959 (mmt) REVERT: F 145 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8081 (pttm) REVERT: F 181 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8367 (pt) REVERT: F 199 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8267 (ttmt) outliers start: 31 outliers final: 21 residues processed: 132 average time/residue: 0.1728 time to fit residues: 36.3273 Evaluate side-chains 123 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 78 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 E residue 181 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 H residue 32 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.083524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069399 restraints weight = 35372.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070177 restraints weight = 28191.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.071042 restraints weight = 22288.716| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11703 Z= 0.136 Angle : 0.526 10.581 16172 Z= 0.266 Chirality : 0.047 0.139 2081 Planarity : 0.004 0.044 2091 Dihedral : 4.094 32.046 1835 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 3.96 % Allowed : 15.70 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1809 helix: 1.72 (0.18), residues: 951 sheet: 0.23 (0.27), residues: 375 loop : -0.29 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 167 HIS 0.003 0.001 HIS H 111 PHE 0.010 0.001 PHE C 32 TYR 0.023 0.002 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 650) hydrogen bonds : angle 4.02031 ( 1860) SS BOND : bond 0.00266 ( 9) SS BOND : angle 2.38496 ( 18) covalent geometry : bond 0.00317 (11694) covalent geometry : angle 0.52013 (16154) *********************** 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 134 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8625 (mmm) cc_final: 0.8286 (mmm) REVERT: A 137 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9032 (mt) REVERT: F 144 MET cc_start: 0.8847 (mmm) cc_final: 0.7944 (mmt) REVERT: F 145 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8061 (pttm) REVERT: F 181 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8175 (pt) outliers start: 30 outliers final: 24 residues processed: 127 average time/residue: 0.1763 time to fit residues: 35.8233 Evaluate side-chains 125 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 78 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 44 THR Chi-restraints excluded: chain F residue 112 MET 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 116 ILE 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 Chi-restraints excluded: chain I residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 84 optimal weight: 0.0030 chunk 144 optimal weight: 0.0980 chunk 127 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 160 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.085283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070695 restraints weight = 34632.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071353 restraints weight = 26193.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072180 restraints weight = 20760.363| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11703 Z= 0.100 Angle : 0.501 10.390 16172 Z= 0.252 Chirality : 0.046 0.135 2081 Planarity : 0.004 0.041 2091 Dihedral : 3.933 32.043 1835 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 16.62 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1809 helix: 1.82 (0.18), residues: 951 sheet: 0.40 (0.27), residues: 345 loop : -0.22 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 167 HIS 0.002 0.000 HIS H 111 PHE 0.010 0.001 PHE C 32 TYR 0.017 0.001 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02265 ( 650) hydrogen bonds : angle 3.87166 ( 1860) SS BOND : bond 0.00226 ( 9) SS BOND : angle 2.06216 ( 18) covalent geometry : bond 0.00223 (11694) covalent geometry : angle 0.49667 (16154) *********************** 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 130 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: D 136 GLU cc_start: 0.8664 (pt0) cc_final: 0.8216 (tt0) REVERT: A 128 MET cc_start: 0.8592 (mmm) cc_final: 0.8209 (mmm) REVERT: A 137 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9028 (mt) REVERT: A 147 ILE cc_start: 0.9313 (mm) cc_final: 0.9046 (mm) REVERT: F 144 MET cc_start: 0.8648 (mmm) cc_final: 0.7735 (mmt) REVERT: F 181 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8133 (pt) outliers start: 29 outliers final: 21 residues processed: 121 average time/residue: 0.2035 time to fit residues: 38.9614 Evaluate side-chains 121 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 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 44 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 MET 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 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 105 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 0.0670 chunk 168 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.082516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068399 restraints weight = 35507.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.069441 restraints weight = 27676.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070208 restraints weight = 21506.376| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11703 Z= 0.165 Angle : 0.552 14.900 16172 Z= 0.277 Chirality : 0.047 0.150 2081 Planarity : 0.004 0.042 2091 Dihedral : 4.082 31.921 1835 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 3.17 % Allowed : 17.28 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1809 helix: 1.77 (0.18), residues: 951 sheet: -0.17 (0.26), residues: 396 loop : -0.19 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 187 HIS 0.003 0.001 HIS G 91 PHE 0.011 0.001 PHE C 32 TYR 0.021 0.002 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 650) hydrogen bonds : angle 4.03242 ( 1860) SS BOND : bond 0.00309 ( 9) SS BOND : angle 2.33272 ( 18) covalent geometry : bond 0.00387 (11694) covalent geometry : angle 0.54685 (16154) *********************** 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 122 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.597 Fit side-chains REVERT: D 136 GLU cc_start: 0.8713 (pt0) cc_final: 0.8263 (tt0) REVERT: A 128 MET cc_start: 0.8380 (mmm) cc_final: 0.8148 (mmm) REVERT: A 137 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9050 (mt) REVERT: F 144 MET cc_start: 0.8686 (mmm) cc_final: 0.7782 (mmt) REVERT: F 181 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8105 (pt) outliers start: 24 outliers final: 20 residues processed: 116 average time/residue: 0.1981 time to fit residues: 36.5057 Evaluate side-chains 115 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 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 165 CYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 MET 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 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 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 145 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.084261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069926 restraints weight = 34756.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070599 restraints weight = 25954.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071328 restraints weight = 19987.969| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11703 Z= 0.111 Angle : 0.518 13.924 16172 Z= 0.258 Chirality : 0.046 0.150 2081 Planarity : 0.004 0.043 2091 Dihedral : 3.980 31.896 1835 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.17 % Allowed : 17.81 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1809 helix: 1.79 (0.18), residues: 951 sheet: 0.13 (0.27), residues: 375 loop : -0.32 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 167 HIS 0.002 0.001 HIS H 111 PHE 0.010 0.001 PHE C 32 TYR 0.020 0.001 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02429 ( 650) hydrogen bonds : angle 3.92304 ( 1860) SS BOND : bond 0.00251 ( 9) SS BOND : angle 2.23079 ( 18) covalent geometry : bond 0.00255 (11694) covalent geometry : angle 0.51320 (16154) ********************** 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 122 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.806 Fit side-chains REVERT: D 136 GLU cc_start: 0.8722 (pt0) cc_final: 0.8296 (tt0) REVERT: A 128 MET cc_start: 0.8611 (mmm) cc_final: 0.8238 (mmm) REVERT: A 137 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9006 (mt) REVERT: A 147 ILE cc_start: 0.9316 (mm) cc_final: 0.9016 (mm) REVERT: F 144 MET cc_start: 0.8595 (mmm) cc_final: 0.7735 (mmt) REVERT: F 181 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8056 (pt) REVERT: F 199 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8609 (ttmt) outliers start: 24 outliers final: 21 residues processed: 115 average time/residue: 0.2174 time to fit residues: 40.2197 Evaluate side-chains 119 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 58 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 165 CYS Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 MET 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 59 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 39 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 56 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 147 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.083148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068779 restraints weight = 34951.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069712 restraints weight = 28247.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.070280 restraints weight = 21880.024| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11703 Z= 0.128 Angle : 0.521 13.683 16172 Z= 0.260 Chirality : 0.047 0.141 2081 Planarity : 0.004 0.043 2091 Dihedral : 3.959 31.844 1835 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.14 % Rotamer: Outliers : 2.90 % Allowed : 18.34 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1809 helix: 1.79 (0.18), residues: 951 sheet: -0.14 (0.27), residues: 366 loop : -0.16 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 187 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE H 77 TYR 0.022 0.001 TYR A 138 ARG 0.002 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.02499 ( 650) hydrogen bonds : angle 3.92200 ( 1860) SS BOND : bond 0.00235 ( 9) SS BOND : angle 2.12419 ( 18) covalent geometry : bond 0.00299 (11694) covalent geometry : angle 0.51678 (16154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7453.13 seconds wall clock time: 135 minutes 45.59 seconds (8145.59 seconds total)