Starting phenix.real_space_refine on Fri Feb 6 12:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405.map" model { file = "/net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nh7_49405/02_2026/9nh7_49405_trim.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 8136 2.51 5 N 2237 2.21 5 O 2546 1.98 5 H 11465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24438 Number of models: 1 Model: "" Number of chains: 17 Chain: "E" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 484 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 2, 'PHE:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 167 Chain: "A" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4935 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4926 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 4927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4927 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1363 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2459 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 34 Chain: "H" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2469 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2484 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.44, per 1000 atoms: 0.18 Number of scatterers: 24438 At special positions: 0 Unit cell: (101.64, 110.88, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 2546 8.00 N 2237 7.00 C 8136 6.00 H 11465 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS G 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS H 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.04 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS I 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.04 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 401 " - " ASN A 171 " " NAG A 402 " - " ASN A 21 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 33 " " NAG B 401 " - " ASN B 171 " " NAG B 402 " - " ASN B 21 " " NAG B 403 " - " ASN B 278 " " NAG B 404 " - " ASN B 33 " " NAG C 401 " - " ASN C 171 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 278 " " NAG C 404 " - " ASN C 33 " " NAG D 1 " - " ASN A 97 " " NAG J 1 " - " ASN A 296 " " NAG K 1 " - " ASN B 97 " " NAG L 1 " - " ASN B 296 " " NAG M 1 " - " ASN C 97 " " NAG N 1 " - " ASN C 296 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 854.5 milliseconds 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3046 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 38 sheets defined 27.4% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.588A pdb=" N LEU E 31 " --> pdb=" O TYR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 105 through 109 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 83 removed outlier: 4.940A pdb=" N SER A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.711A pdb=" N GLU B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 82 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 193 through 202 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.580A pdb=" N GLU C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 82 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.738A pdb=" N LEU F 31 " --> pdb=" O TYR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 56 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 59 removed outlier: 3.553A pdb=" N GLY G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 126 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.759A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.666A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 171 " --> pdb=" O LYS G 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 59 removed outlier: 3.562A pdb=" N MET H 59 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 127 Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.997A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 172 removed outlier: 4.505A pdb=" N ASN H 169 " --> pdb=" O GLU H 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 59 removed outlier: 3.607A pdb=" N MET I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 170 removed outlier: 4.050A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.264A pdb=" N ALA E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 38 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR E 111 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 31 through 36 removed outlier: 4.208A pdb=" N GLY G 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 13 " --> pdb=" O PHE G 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.415A pdb=" N LEU A 51 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N CYS A 284 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.502A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 125 removed outlier: 7.068A pdb=" N SER A 267 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 121 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA A 265 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG A 123 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 263 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A 186 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 239 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 137 through 138 Processing sheet with id=AB2, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.751A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 152 " --> pdb=" O CYS A 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AB4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.342A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 31 through 36 removed outlier: 3.709A pdb=" N GLY H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.934A pdb=" N ASP B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.490A pdb=" N LEU B 51 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N CYS B 284 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.353A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 118 through 125 removed outlier: 6.910A pdb=" N SER B 267 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 121 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA B 265 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 123 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 263 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 181 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU B 257 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 160 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 125 removed outlier: 6.910A pdb=" N SER B 267 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 121 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA B 265 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 123 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 263 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 181 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.239A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AC6, first strand: chain 'B' and resid 294 through 295 removed outlier: 4.380A pdb=" N CYS B 288 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY B 310 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR H 64 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B 312 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 31 through 36 removed outlier: 3.570A pdb=" N ALA I 35 " --> pdb=" O TYR I 24 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY I 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 13 " --> pdb=" O PHE I 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.963A pdb=" N LEU C 51 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.396A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 125 removed outlier: 6.486A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 118 through 125 removed outlier: 6.486A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AD7, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.588A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 170 through 175 removed outlier: 3.548A pdb=" N ALA C 253 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.614A pdb=" N CYS C 312 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.204A pdb=" N ALA F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG F 38 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR F 111 " --> pdb=" O ALA F 98 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11465 1.04 - 1.24: 1857 1.24 - 1.44: 4043 1.44 - 1.64: 7270 1.64 - 1.84: 76 Bond restraints: 24711 Sorted by residual: bond pdb=" C1 NAG B 404 " pdb=" O5 NAG B 404 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C GLU C 311 " pdb=" N CYS C 312 " ideal model delta sigma weight residual 1.327 1.252 0.075 1.71e-02 3.42e+03 1.90e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" C5 NAG B 404 " pdb=" O5 NAG B 404 " ideal model delta sigma weight residual 1.413 1.453 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sigma weight residual 1.417 1.454 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 24706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 43725 2.37 - 4.74: 241 4.74 - 7.11: 25 7.11 - 9.47: 3 9.47 - 11.84: 1 Bond angle restraints: 43995 Sorted by residual: angle pdb=" C1 NAG B 404 " pdb=" O5 NAG B 404 " pdb=" C5 NAG B 404 " ideal model delta sigma weight residual 113.21 125.05 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA CYS C 14 " pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " ideal model delta sigma weight residual 114.40 122.43 -8.03 2.30e+00 1.89e-01 1.22e+01 angle pdb=" N CYS C 14 " pdb=" CA CYS C 14 " pdb=" C CYS C 14 " ideal model delta sigma weight residual 108.14 113.07 -4.93 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N ASN B 296 " pdb=" CA ASN B 296 " pdb=" CB ASN B 296 " ideal model delta sigma weight residual 111.39 106.85 4.54 1.56e+00 4.11e-01 8.49e+00 angle pdb=" N GLY G 134 " pdb=" CA GLY G 134 " pdb=" C GLY G 134 " ideal model delta sigma weight residual 112.45 106.41 6.04 2.10e+00 2.27e-01 8.26e+00 ... (remaining 43990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 11210 22.13 - 44.26: 693 44.26 - 66.38: 266 66.38 - 88.51: 51 88.51 - 110.64: 22 Dihedral angle restraints: 12242 sinusoidal: 6591 harmonic: 5651 Sorted by residual: dihedral pdb=" CA ASN E 74 " pdb=" C ASN E 74 " pdb=" N SER E 75 " pdb=" CA SER E 75 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE A 295 " pdb=" C ILE A 295 " pdb=" N ASN A 296 " pdb=" CA ASN A 296 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS I 137 " pdb=" CB CYS I 137 " ideal model delta sinusoidal sigma weight residual 93.00 57.96 35.04 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 12239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 2043 0.198 - 0.396: 8 0.396 - 0.594: 1 0.594 - 0.793: 0 0.793 - 0.991: 1 Chirality restraints: 2053 Sorted by residual: chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 33 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" C3 NAG B 404 " pdb=" C2 NAG B 404 " pdb=" C4 NAG B 404 " pdb=" O3 NAG B 404 " both_signs ideal model delta sigma weight residual False 2.45 2.01 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.35e+00 ... (remaining 2050 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 295 " -0.043 2.00e-02 2.50e+03 7.67e-02 5.89e+01 pdb=" N ASN B 296 " 0.132 2.00e-02 2.50e+03 pdb=" CA ASN B 296 " -0.035 2.00e-02 2.50e+03 pdb=" H ASN B 296 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 404 " -0.032 2.00e-02 2.50e+03 2.59e-02 8.38e+00 pdb=" C7 NAG B 404 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B 404 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B 404 " 0.041 2.00e-02 2.50e+03 pdb=" O7 NAG B 404 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.023 2.00e-02 2.50e+03 2.05e-02 5.24e+00 pdb=" C7 NAG L 1 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.022 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.025 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.002 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 804 2.15 - 2.76: 43736 2.76 - 3.38: 63919 3.38 - 3.99: 84867 3.99 - 4.60: 133730 Nonbonded interactions: 327056 Sorted by model distance: nonbonded pdb=" O ILE C 71 " pdb="HD21 ASN C 156 " model vdw 1.539 2.450 nonbonded pdb=" HH TYR B 154 " pdb=" OH TYR B 238 " model vdw 1.547 2.450 nonbonded pdb=" HH TYR A 154 " pdb=" OH TYR A 238 " model vdw 1.559 2.450 nonbonded pdb=" OD2 ASP A 11 " pdb=" H CYS G 144 " model vdw 1.560 2.450 nonbonded pdb=" OE1 GLU C 181 " pdb="HH21 ARG C 268 " model vdw 1.565 2.450 ... (remaining 327051 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 11 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 295 or (resid \ 296 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 297 throug \ h 404)) selection = chain 'B' selection = (chain 'C' and (resid 11 through 295 or (resid 296 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 297 through 404)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = (chain 'F' and ((resid 2 through 14 and (name N or name CA or name C or name O o \ r name CB )) or (resid 15 through 16 and (name N or name CA or name C or name O \ )) or (resid 17 through 25 and (name N or name CA or name C or name O or name CB \ )) or (resid 26 and (name N or name CA or name C or name O )) or (resid 27 thro \ ugh 34 and (name N or name CA or name C or name O or name CB )) or (resid 35 and \ (name N or name CA or name C or name O )) or (resid 36 through 40 and (name N o \ r name CA or name C or name O or name CB )) or (resid 44 and (name N or name CA \ or name C or name O )) or (resid 45 through 54 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 (resid 56 through 65 and (name N or name CA or name C or name O or name CB \ )) or (resid 66 and (name N or name CA or name C or name O )) or (resid 67 thro \ ugh 104 and (name N or name CA or name C or name O or name CB )) or (resid 105 a \ nd (name N or name CA or name C or name O )) or (resid 106 and (name N or name C \ A or name C or name O or name CB )) or (resid 107 and (name N or name CA or name \ C or name O )) or (resid 108 through 112 and (name N or name CA or name C or na \ me O or name CB )) or (resid 113 and (name N or name CA or name C or name O )) o \ r (resid 114 and (name N or name CA or name C or name O or name CB )) or (resid \ 115 and (name N or name CA or name C or name O )) or (resid 116 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and (resid 9 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 20 through 173)) selection = (chain 'H' and (resid 9 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 154 through 173)) selection = (chain 'I' and (resid 9 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 40 through 152 or (resid \ 153 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 154 through 173)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.090 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 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 : 0.005 0.116 13291 Z= 0.228 Angle : 0.719 14.455 18103 Z= 0.352 Chirality : 0.052 0.991 2053 Planarity : 0.004 0.040 2297 Dihedral : 15.715 110.638 5098 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.16 % Allowed : 8.11 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1628 helix: 1.54 (0.27), residues: 378 sheet: -0.65 (0.27), residues: 350 loop : -1.36 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 218 TYR 0.018 0.002 TYR A 174 PHE 0.016 0.002 PHE B 121 TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00492 (13246) covalent geometry : angle 0.66333 (17984) SS BOND : bond 0.00474 ( 16) SS BOND : angle 1.24636 ( 32) hydrogen bonds : bond 0.22252 ( 533) hydrogen bonds : angle 7.85987 ( 1482) link_BETA1-4 : bond 0.00708 ( 11) link_BETA1-4 : angle 3.13350 ( 33) link_NAG-ASN : bond 0.01441 ( 18) link_NAG-ASN : angle 4.44907 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ILE cc_start: 0.8144 (mt) cc_final: 0.7846 (mm) REVERT: B 113 GLU cc_start: 0.7351 (tp30) cc_final: 0.7082 (tp30) REVERT: B 202 GLN cc_start: 0.7606 (mm110) cc_final: 0.7401 (mm-40) REVERT: B 220 THR cc_start: 0.7679 (p) cc_final: 0.7243 (m) REVERT: B 225 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6598 (mm-30) REVERT: H 71 ASN cc_start: 0.7276 (t0) cc_final: 0.6723 (t0) REVERT: H 116 LYS cc_start: 0.7353 (ttmm) cc_final: 0.7129 (ttmm) REVERT: I 81 ASN cc_start: 0.7944 (t0) cc_final: 0.7650 (t0) REVERT: I 85 ASP cc_start: 0.7316 (m-30) cc_final: 0.7051 (m-30) REVERT: I 106 ARG cc_start: 0.6851 (mtt90) cc_final: 0.6503 (mtt90) REVERT: I 114 ASN cc_start: 0.7583 (m-40) cc_final: 0.7315 (m-40) REVERT: I 124 ASN cc_start: 0.7544 (m-40) cc_final: 0.6980 (m-40) outliers start: 2 outliers final: 1 residues processed: 344 average time/residue: 0.3215 time to fit residues: 146.8315 Evaluate side-chains 294 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 216 ASN B 189 HIS B 214 ASN C 189 HIS C 282 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121233 restraints weight = 46772.018| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.31 r_work: 0.3414 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 13291 Z= 0.383 Angle : 0.908 11.006 18103 Z= 0.470 Chirality : 0.057 0.411 2053 Planarity : 0.007 0.076 2297 Dihedral : 8.641 58.581 2375 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.18 % Allowed : 12.16 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1628 helix: 1.11 (0.26), residues: 381 sheet: -0.69 (0.27), residues: 330 loop : -1.92 (0.16), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 230 TYR 0.032 0.003 TYR F 109 PHE 0.021 0.003 PHE B 121 TRP 0.018 0.002 TRP H 26 HIS 0.012 0.003 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00895 (13246) covalent geometry : angle 0.87460 (17984) SS BOND : bond 0.00719 ( 16) SS BOND : angle 2.87781 ( 32) hydrogen bonds : bond 0.05963 ( 533) hydrogen bonds : angle 5.78178 ( 1482) link_BETA1-4 : bond 0.00509 ( 11) link_BETA1-4 : angle 3.29224 ( 33) link_NAG-ASN : bond 0.01012 ( 18) link_NAG-ASN : angle 3.19570 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7597 (m-30) cc_final: 0.7390 (m-30) REVERT: A 40 VAL cc_start: 0.8482 (t) cc_final: 0.8219 (m) REVERT: A 46 SER cc_start: 0.8469 (m) cc_final: 0.8029 (p) REVERT: A 119 SER cc_start: 0.8560 (t) cc_final: 0.8331 (p) REVERT: A 136 HIS cc_start: 0.8116 (m170) cc_final: 0.7689 (m-70) REVERT: A 177 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7515 (mmtm) REVERT: A 214 ASN cc_start: 0.7700 (t0) cc_final: 0.7467 (t0) REVERT: B 220 THR cc_start: 0.8061 (p) cc_final: 0.7653 (m) REVERT: C 41 ASN cc_start: 0.7974 (t0) cc_final: 0.7751 (t0) REVERT: C 162 GLU cc_start: 0.6971 (pp20) cc_final: 0.6533 (pp20) REVERT: G 113 SER cc_start: 0.7799 (m) cc_final: 0.7591 (p) REVERT: H 90 ASP cc_start: 0.7755 (m-30) cc_final: 0.7384 (m-30) REVERT: H 114 ASN cc_start: 0.8152 (m-40) cc_final: 0.7528 (m-40) REVERT: H 116 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7330 (ttmm) REVERT: I 106 ARG cc_start: 0.7013 (mtt90) cc_final: 0.6746 (mtt90) REVERT: I 112 ASP cc_start: 0.7126 (m-30) cc_final: 0.6864 (m-30) REVERT: I 114 ASN cc_start: 0.7769 (m-40) cc_final: 0.7331 (m110) REVERT: I 124 ASN cc_start: 0.7734 (m-40) cc_final: 0.7511 (m110) outliers start: 28 outliers final: 20 residues processed: 344 average time/residue: 0.3207 time to fit residues: 146.4775 Evaluate side-chains 330 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN C 232 GLN H 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119957 restraints weight = 46647.615| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.27 r_work: 0.3401 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 13291 Z= 0.185 Angle : 0.677 32.699 18103 Z= 0.347 Chirality : 0.044 0.406 2053 Planarity : 0.004 0.047 2297 Dihedral : 7.177 57.368 2375 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.95 % Allowed : 13.72 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1628 helix: 1.67 (0.27), residues: 381 sheet: -0.41 (0.27), residues: 330 loop : -1.70 (0.17), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.013 0.002 TYR B 239 PHE 0.018 0.001 PHE C 121 TRP 0.007 0.001 TRP B 133 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00438 (13246) covalent geometry : angle 0.63133 (17984) SS BOND : bond 0.01679 ( 16) SS BOND : angle 4.42526 ( 32) hydrogen bonds : bond 0.05507 ( 533) hydrogen bonds : angle 5.31443 ( 1482) link_BETA1-4 : bond 0.00444 ( 11) link_BETA1-4 : angle 1.96612 ( 33) link_NAG-ASN : bond 0.00393 ( 18) link_NAG-ASN : angle 2.64593 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8092 (mttm) cc_final: 0.7867 (mmtm) REVERT: A 40 VAL cc_start: 0.8470 (t) cc_final: 0.8191 (m) REVERT: A 46 SER cc_start: 0.8506 (m) cc_final: 0.8054 (p) REVERT: A 118 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8149 (t) REVERT: A 119 SER cc_start: 0.8551 (t) cc_final: 0.8290 (p) REVERT: A 136 HIS cc_start: 0.8177 (m170) cc_final: 0.7703 (m-70) REVERT: A 214 ASN cc_start: 0.7760 (t0) cc_final: 0.7514 (t0) REVERT: B 48 ASN cc_start: 0.7949 (t0) cc_final: 0.7708 (t0) REVERT: B 50 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7883 (mtmm) REVERT: B 202 GLN cc_start: 0.8364 (mm110) cc_final: 0.8123 (mm110) REVERT: B 220 THR cc_start: 0.8041 (p) cc_final: 0.7666 (m) REVERT: C 41 ASN cc_start: 0.7961 (t0) cc_final: 0.7670 (t0) REVERT: C 162 GLU cc_start: 0.7201 (pp20) cc_final: 0.6765 (pp20) REVERT: C 292 GLN cc_start: 0.7975 (mt0) cc_final: 0.7761 (mt0) REVERT: H 90 ASP cc_start: 0.7694 (m-30) cc_final: 0.7437 (m-30) REVERT: H 114 ASN cc_start: 0.8161 (m-40) cc_final: 0.7567 (m-40) REVERT: I 75 LYS cc_start: 0.8525 (tptm) cc_final: 0.8307 (tptm) REVERT: I 97 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7465 (mp0) REVERT: I 106 ARG cc_start: 0.7110 (mtt90) cc_final: 0.6815 (mtt90) REVERT: I 114 ASN cc_start: 0.7760 (m-40) cc_final: 0.7338 (m110) REVERT: I 124 ASN cc_start: 0.7746 (m-40) cc_final: 0.7481 (m110) outliers start: 25 outliers final: 17 residues processed: 328 average time/residue: 0.3263 time to fit residues: 141.5077 Evaluate side-chains 325 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN G 53 ASN H 50 ASN H 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117143 restraints weight = 46646.163| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.31 r_work: 0.3360 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13291 Z= 0.260 Angle : 0.654 18.288 18103 Z= 0.346 Chirality : 0.045 0.285 2053 Planarity : 0.004 0.046 2297 Dihedral : 6.691 59.863 2375 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.95 % Allowed : 14.96 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1628 helix: 1.63 (0.27), residues: 387 sheet: -0.35 (0.27), residues: 330 loop : -1.71 (0.17), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 230 TYR 0.022 0.002 TYR F 109 PHE 0.020 0.002 PHE B 121 TRP 0.010 0.002 TRP C 186 HIS 0.008 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00615 (13246) covalent geometry : angle 0.62994 (17984) SS BOND : bond 0.00781 ( 16) SS BOND : angle 2.41995 ( 32) hydrogen bonds : bond 0.05238 ( 533) hydrogen bonds : angle 5.18831 ( 1482) link_BETA1-4 : bond 0.00707 ( 11) link_BETA1-4 : angle 1.63481 ( 33) link_NAG-ASN : bond 0.00488 ( 18) link_NAG-ASN : angle 2.51836 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 320 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8115 (mttm) cc_final: 0.7861 (mmtm) REVERT: A 46 SER cc_start: 0.8568 (m) cc_final: 0.8063 (p) REVERT: A 53 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8167 (mtm-85) REVERT: A 84 ARG cc_start: 0.7071 (mmt-90) cc_final: 0.6689 (mpt180) REVERT: A 119 SER cc_start: 0.8389 (t) cc_final: 0.8149 (p) REVERT: A 175 VAL cc_start: 0.8384 (p) cc_final: 0.8168 (t) REVERT: A 214 ASN cc_start: 0.7724 (t0) cc_final: 0.7483 (t0) REVERT: A 244 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8286 (mtmt) REVERT: A 281 MET cc_start: 0.7786 (tpp) cc_final: 0.7578 (tpt) REVERT: B 48 ASN cc_start: 0.7940 (t0) cc_final: 0.7658 (t0) REVERT: B 50 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7888 (mtmm) REVERT: B 202 GLN cc_start: 0.8411 (mm110) cc_final: 0.8133 (mm110) REVERT: B 220 THR cc_start: 0.8084 (p) cc_final: 0.7723 (m) REVERT: C 41 ASN cc_start: 0.8078 (t0) cc_final: 0.7739 (t0) REVERT: C 162 GLU cc_start: 0.7469 (pp20) cc_final: 0.6854 (pp20) REVERT: C 200 LEU cc_start: 0.7891 (mt) cc_final: 0.7683 (mt) REVERT: G 124 ASN cc_start: 0.7637 (m-40) cc_final: 0.7370 (m-40) REVERT: H 27 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: H 50 ASN cc_start: 0.7758 (m-40) cc_final: 0.7422 (m-40) REVERT: H 90 ASP cc_start: 0.7652 (m-30) cc_final: 0.7378 (m-30) REVERT: I 97 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7464 (mp0) REVERT: I 106 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6914 (mtt90) REVERT: I 114 ASN cc_start: 0.7736 (m-40) cc_final: 0.7349 (m110) REVERT: I 124 ASN cc_start: 0.7776 (m-40) cc_final: 0.7495 (m110) REVERT: I 161 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7505 (mmmt) outliers start: 25 outliers final: 20 residues processed: 338 average time/residue: 0.3169 time to fit residues: 142.2142 Evaluate side-chains 333 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 102 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 28 ASN G 53 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117891 restraints weight = 46390.109| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.31 r_work: 0.3373 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13291 Z= 0.155 Angle : 0.555 9.388 18103 Z= 0.293 Chirality : 0.042 0.299 2053 Planarity : 0.004 0.039 2297 Dihedral : 6.222 59.803 2375 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 15.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1628 helix: 1.87 (0.27), residues: 387 sheet: -0.32 (0.28), residues: 330 loop : -1.63 (0.17), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 76 TYR 0.013 0.001 TYR B 239 PHE 0.018 0.001 PHE A 121 TRP 0.008 0.001 TRP B 133 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00362 (13246) covalent geometry : angle 0.52957 (17984) SS BOND : bond 0.00705 ( 16) SS BOND : angle 2.14731 ( 32) hydrogen bonds : bond 0.04634 ( 533) hydrogen bonds : angle 4.99061 ( 1482) link_BETA1-4 : bond 0.00384 ( 11) link_BETA1-4 : angle 1.49712 ( 33) link_NAG-ASN : bond 0.00318 ( 18) link_NAG-ASN : angle 2.38087 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 316 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8119 (mttm) cc_final: 0.7863 (mmtm) REVERT: A 46 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 53 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: A 84 ARG cc_start: 0.7080 (mmt-90) cc_final: 0.6715 (mpt180) REVERT: A 119 SER cc_start: 0.8352 (t) cc_final: 0.8144 (p) REVERT: A 175 VAL cc_start: 0.8330 (p) cc_final: 0.8121 (t) REVERT: A 214 ASN cc_start: 0.7697 (t0) cc_final: 0.7456 (t0) REVERT: B 48 ASN cc_start: 0.7922 (t0) cc_final: 0.7644 (t0) REVERT: B 50 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7855 (mtmm) REVERT: B 202 GLN cc_start: 0.8404 (mm110) cc_final: 0.8153 (mm110) REVERT: B 220 THR cc_start: 0.8066 (p) cc_final: 0.7713 (m) REVERT: C 41 ASN cc_start: 0.8102 (t0) cc_final: 0.7780 (t0) REVERT: C 162 GLU cc_start: 0.7452 (pp20) cc_final: 0.6796 (pp20) REVERT: C 200 LEU cc_start: 0.7878 (mt) cc_final: 0.7657 (mt) REVERT: G 69 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7391 (mm-30) REVERT: H 50 ASN cc_start: 0.7872 (m-40) cc_final: 0.7450 (m-40) REVERT: I 75 LYS cc_start: 0.8406 (tptm) cc_final: 0.8131 (tptp) REVERT: I 97 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7430 (mp0) REVERT: I 106 ARG cc_start: 0.7208 (mtt90) cc_final: 0.6911 (mtt90) REVERT: I 114 ASN cc_start: 0.7700 (m-40) cc_final: 0.7313 (m110) REVERT: I 124 ASN cc_start: 0.7725 (m-40) cc_final: 0.7422 (m110) REVERT: I 161 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7465 (mmmt) outliers start: 29 outliers final: 22 residues processed: 337 average time/residue: 0.3109 time to fit residues: 139.6731 Evaluate side-chains 334 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 214 ASN G 53 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117595 restraints weight = 46672.260| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.28 r_work: 0.3354 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13291 Z= 0.209 Angle : 0.588 11.998 18103 Z= 0.310 Chirality : 0.043 0.248 2053 Planarity : 0.004 0.039 2297 Dihedral : 6.063 58.952 2375 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.73 % Allowed : 15.43 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1628 helix: 1.88 (0.26), residues: 387 sheet: -0.29 (0.28), residues: 330 loop : -1.59 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 317 TYR 0.017 0.002 TYR G 159 PHE 0.018 0.002 PHE B 121 TRP 0.009 0.002 TRP B 133 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00492 (13246) covalent geometry : angle 0.56530 (17984) SS BOND : bond 0.00807 ( 16) SS BOND : angle 2.18495 ( 32) hydrogen bonds : bond 0.04774 ( 533) hydrogen bonds : angle 5.00200 ( 1482) link_BETA1-4 : bond 0.00412 ( 11) link_BETA1-4 : angle 1.49629 ( 33) link_NAG-ASN : bond 0.00375 ( 18) link_NAG-ASN : angle 2.26177 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8086 (mttm) cc_final: 0.7870 (mmtm) REVERT: A 44 GLU cc_start: 0.7647 (tp30) cc_final: 0.7362 (tp30) REVERT: A 46 SER cc_start: 0.8555 (m) cc_final: 0.8197 (p) REVERT: A 214 ASN cc_start: 0.7675 (t0) cc_final: 0.7416 (t0) REVERT: B 202 GLN cc_start: 0.8414 (mm110) cc_final: 0.8171 (mm110) REVERT: B 220 THR cc_start: 0.8048 (p) cc_final: 0.7697 (m) REVERT: C 29 VAL cc_start: 0.7783 (m) cc_final: 0.7577 (t) REVERT: C 195 LYS cc_start: 0.7877 (tttp) cc_final: 0.7661 (tttp) REVERT: C 200 LEU cc_start: 0.7921 (mt) cc_final: 0.7681 (mt) REVERT: G 69 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7426 (mm-30) REVERT: G 151 SER cc_start: 0.8036 (p) cc_final: 0.7672 (t) REVERT: H 132 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7387 (mm-30) REVERT: I 75 LYS cc_start: 0.8432 (tptm) cc_final: 0.8172 (tptp) REVERT: I 97 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7416 (mp0) REVERT: I 106 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6912 (mtt90) REVERT: I 114 ASN cc_start: 0.7711 (m-40) cc_final: 0.7340 (m110) REVERT: I 124 ASN cc_start: 0.7768 (m-40) cc_final: 0.7494 (m110) REVERT: I 161 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7484 (mmmt) outliers start: 35 outliers final: 29 residues processed: 346 average time/residue: 0.3179 time to fit residues: 146.2099 Evaluate side-chains 350 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 321 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 3 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117931 restraints weight = 46372.000| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.28 r_work: 0.3365 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13291 Z= 0.171 Angle : 0.558 10.772 18103 Z= 0.295 Chirality : 0.042 0.266 2053 Planarity : 0.004 0.038 2297 Dihedral : 5.883 58.802 2375 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.42 % Allowed : 16.37 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1628 helix: 2.02 (0.26), residues: 387 sheet: -0.50 (0.27), residues: 348 loop : -1.49 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 127 TYR 0.017 0.001 TYR G 159 PHE 0.018 0.001 PHE B 121 TRP 0.009 0.001 TRP B 133 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00401 (13246) covalent geometry : angle 0.53528 (17984) SS BOND : bond 0.00829 ( 16) SS BOND : angle 2.18089 ( 32) hydrogen bonds : bond 0.04545 ( 533) hydrogen bonds : angle 4.93181 ( 1482) link_BETA1-4 : bond 0.00410 ( 11) link_BETA1-4 : angle 1.43043 ( 33) link_NAG-ASN : bond 0.00314 ( 18) link_NAG-ASN : angle 2.23324 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8092 (mttm) cc_final: 0.7862 (mmtm) REVERT: A 44 GLU cc_start: 0.7636 (tp30) cc_final: 0.7302 (tp30) REVERT: A 46 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8224 (p) REVERT: A 214 ASN cc_start: 0.7672 (t0) cc_final: 0.7422 (t0) REVERT: B 202 GLN cc_start: 0.8398 (mm110) cc_final: 0.8153 (mm110) REVERT: B 220 THR cc_start: 0.8032 (p) cc_final: 0.7695 (m) REVERT: C 195 LYS cc_start: 0.7882 (tttp) cc_final: 0.7669 (tttp) REVERT: C 200 LEU cc_start: 0.7946 (mt) cc_final: 0.7690 (mt) REVERT: G 19 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7413 (t0) REVERT: G 69 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7383 (mm-30) REVERT: G 151 SER cc_start: 0.8040 (p) cc_final: 0.7698 (t) REVERT: H 118 LEU cc_start: 0.8261 (tp) cc_final: 0.8060 (tt) REVERT: H 132 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7346 (mm-30) REVERT: I 97 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7376 (mp0) REVERT: I 106 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6904 (mtt90) REVERT: I 114 ASN cc_start: 0.7706 (m-40) cc_final: 0.7335 (m110) REVERT: I 124 ASN cc_start: 0.7781 (m-40) cc_final: 0.7502 (m110) REVERT: I 161 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7457 (mmmt) outliers start: 31 outliers final: 21 residues processed: 337 average time/residue: 0.3414 time to fit residues: 151.8923 Evaluate side-chains 342 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116839 restraints weight = 46474.559| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.27 r_work: 0.3352 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13291 Z= 0.223 Angle : 0.587 11.492 18103 Z= 0.311 Chirality : 0.043 0.224 2053 Planarity : 0.004 0.039 2297 Dihedral : 5.817 59.463 2375 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.96 % Allowed : 15.43 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1628 helix: 1.97 (0.26), residues: 387 sheet: -0.53 (0.27), residues: 348 loop : -1.53 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.016 0.002 TYR F 109 PHE 0.025 0.002 PHE G 140 TRP 0.010 0.002 TRP B 133 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00523 (13246) covalent geometry : angle 0.56652 (17984) SS BOND : bond 0.00866 ( 16) SS BOND : angle 2.16034 ( 32) hydrogen bonds : bond 0.04768 ( 533) hydrogen bonds : angle 5.00566 ( 1482) link_BETA1-4 : bond 0.00445 ( 11) link_BETA1-4 : angle 1.45956 ( 33) link_NAG-ASN : bond 0.00342 ( 18) link_NAG-ASN : angle 2.18088 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 361 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 53 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8052 (mtm180) REVERT: A 214 ASN cc_start: 0.7660 (t0) cc_final: 0.7418 (t0) REVERT: B 177 LYS cc_start: 0.8311 (mmmm) cc_final: 0.7977 (mmmm) REVERT: B 202 GLN cc_start: 0.8401 (mm110) cc_final: 0.8142 (mm110) REVERT: B 220 THR cc_start: 0.8073 (p) cc_final: 0.7739 (m) REVERT: C 166 SER cc_start: 0.7581 (m) cc_final: 0.7373 (p) REVERT: C 195 LYS cc_start: 0.7904 (tttp) cc_final: 0.7691 (tttp) REVERT: G 69 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7355 (mm-30) REVERT: G 151 SER cc_start: 0.8061 (p) cc_final: 0.7739 (t) REVERT: H 132 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7357 (mm-30) REVERT: I 81 ASN cc_start: 0.8695 (t0) cc_final: 0.8473 (t0) REVERT: I 97 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7409 (mp0) REVERT: I 106 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6942 (mtt90) REVERT: I 114 ASN cc_start: 0.7719 (m-40) cc_final: 0.7372 (m110) REVERT: I 124 ASN cc_start: 0.7805 (m-40) cc_final: 0.7544 (m110) REVERT: I 161 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7489 (mmmt) outliers start: 38 outliers final: 29 residues processed: 341 average time/residue: 0.3456 time to fit residues: 154.7336 Evaluate side-chains 348 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 318 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.0060 chunk 138 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115426 restraints weight = 47218.382| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.33 r_work: 0.3326 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13291 Z= 0.186 Angle : 0.564 10.575 18103 Z= 0.298 Chirality : 0.042 0.243 2053 Planarity : 0.004 0.038 2297 Dihedral : 5.626 59.980 2375 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.34 % Allowed : 16.76 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1628 helix: 2.03 (0.27), residues: 387 sheet: -0.46 (0.27), residues: 348 loop : -1.49 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.014 0.001 TYR C 215 PHE 0.018 0.001 PHE B 121 TRP 0.009 0.001 TRP B 133 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00437 (13246) covalent geometry : angle 0.54367 (17984) SS BOND : bond 0.00768 ( 16) SS BOND : angle 2.01570 ( 32) hydrogen bonds : bond 0.04561 ( 533) hydrogen bonds : angle 4.95777 ( 1482) link_BETA1-4 : bond 0.00402 ( 11) link_BETA1-4 : angle 1.38786 ( 33) link_NAG-ASN : bond 0.00309 ( 18) link_NAG-ASN : angle 2.14770 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7684 (tp30) cc_final: 0.7357 (tp30) REVERT: A 46 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 53 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8029 (mtm180) REVERT: A 214 ASN cc_start: 0.7701 (t0) cc_final: 0.7452 (t0) REVERT: B 177 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7972 (mmmm) REVERT: B 202 GLN cc_start: 0.8409 (mm110) cc_final: 0.8143 (mm110) REVERT: B 220 THR cc_start: 0.8053 (p) cc_final: 0.7710 (m) REVERT: C 195 LYS cc_start: 0.7948 (tttp) cc_final: 0.7702 (tttp) REVERT: G 69 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7353 (mm-30) REVERT: G 151 SER cc_start: 0.8096 (p) cc_final: 0.7808 (t) REVERT: H 132 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7389 (mm-30) REVERT: I 81 ASN cc_start: 0.8691 (t0) cc_final: 0.8458 (t0) REVERT: I 97 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7434 (mp0) REVERT: I 106 ARG cc_start: 0.7273 (mtt90) cc_final: 0.6967 (mtt90) REVERT: I 114 ASN cc_start: 0.7670 (m-40) cc_final: 0.7325 (m110) REVERT: I 124 ASN cc_start: 0.7757 (m-40) cc_final: 0.7477 (m110) REVERT: I 161 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7505 (mmmt) outliers start: 30 outliers final: 25 residues processed: 339 average time/residue: 0.3414 time to fit residues: 152.8299 Evaluate side-chains 349 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 8 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115891 restraints weight = 46862.395| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.34 r_work: 0.3319 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 13291 Z= 0.324 Angle : 0.832 59.182 18103 Z= 0.474 Chirality : 0.046 0.239 2053 Planarity : 0.004 0.040 2297 Dihedral : 5.657 59.975 2375 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.26 % Allowed : 17.15 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1628 helix: 2.02 (0.27), residues: 387 sheet: -0.19 (0.28), residues: 330 loop : -1.53 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 230 TYR 0.016 0.002 TYR C 215 PHE 0.018 0.002 PHE B 121 TRP 0.013 0.002 TRP C 186 HIS 0.006 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00728 (13246) covalent geometry : angle 0.79813 (17984) SS BOND : bond 0.00958 ( 16) SS BOND : angle 4.92971 ( 32) hydrogen bonds : bond 0.04779 ( 533) hydrogen bonds : angle 4.96237 ( 1482) link_BETA1-4 : bond 0.00387 ( 11) link_BETA1-4 : angle 1.41022 ( 33) link_NAG-ASN : bond 0.00380 ( 18) link_NAG-ASN : angle 2.13394 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7691 (tp30) cc_final: 0.7361 (tp30) REVERT: A 46 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 53 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8035 (mtm180) REVERT: A 214 ASN cc_start: 0.7709 (t0) cc_final: 0.7460 (t0) REVERT: B 177 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7986 (mmmm) REVERT: B 220 THR cc_start: 0.8078 (p) cc_final: 0.7746 (m) REVERT: C 195 LYS cc_start: 0.7952 (tttp) cc_final: 0.7719 (tttp) REVERT: G 69 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7350 (mm-30) REVERT: G 151 SER cc_start: 0.8113 (p) cc_final: 0.7828 (t) REVERT: H 132 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7392 (mm-30) REVERT: I 81 ASN cc_start: 0.8703 (t0) cc_final: 0.8473 (t0) REVERT: I 97 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7442 (mp0) REVERT: I 106 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6971 (mtt90) REVERT: I 114 ASN cc_start: 0.7698 (m-40) cc_final: 0.7357 (m110) REVERT: I 124 ASN cc_start: 0.7769 (m-40) cc_final: 0.7489 (m110) REVERT: I 161 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7520 (mmmt) outliers start: 29 outliers final: 27 residues processed: 339 average time/residue: 0.3387 time to fit residues: 151.7241 Evaluate side-chains 353 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115946 restraints weight = 46988.175| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.35 r_work: 0.3318 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 13291 Z= 0.322 Angle : 0.832 59.200 18103 Z= 0.473 Chirality : 0.046 0.239 2053 Planarity : 0.004 0.040 2297 Dihedral : 5.657 59.976 2375 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.18 % Allowed : 17.15 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1628 helix: 2.02 (0.27), residues: 387 sheet: -0.19 (0.28), residues: 330 loop : -1.53 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 230 TYR 0.016 0.002 TYR C 215 PHE 0.018 0.002 PHE B 121 TRP 0.013 0.002 TRP C 186 HIS 0.006 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00726 (13246) covalent geometry : angle 0.79774 (17984) SS BOND : bond 0.00958 ( 16) SS BOND : angle 4.92719 ( 32) hydrogen bonds : bond 0.04776 ( 533) hydrogen bonds : angle 4.96242 ( 1482) link_BETA1-4 : bond 0.00388 ( 11) link_BETA1-4 : angle 1.40986 ( 33) link_NAG-ASN : bond 0.00379 ( 18) link_NAG-ASN : angle 2.13409 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6649.43 seconds wall clock time: 113 minutes 29.40 seconds (6809.40 seconds total)