Starting phenix.real_space_refine on Wed Mar 4 03:51:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwn_26837/03_2026/7uwn_26837.cif" } resolution = 3.01 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6667 2.51 5 N 1898 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 887 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2147 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 853 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1888 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3036 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 7, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 8 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "H" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Chain: "F" 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: "G" 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 Time building chain proxies: 2.64, per 1000 atoms: 0.25 Number of scatterers: 10602 At special positions: 0 Unit cell: (116.194, 133.25, 155.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1965 8.00 N 1898 7.00 C 6667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 294 " distance=2.01 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 83 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 272 " - pdb=" SG CYS G 288 " 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 H 1 " - " NAG H 2 " NAG-ASN " NAG A 201 " - " ASN A 68 " " NAG C 401 " - " ASN C 54 " " NAG C 402 " - " ASN C 225 " " NAG C 403 " - " ASN C 49 " " NAG C 404 " - " ASN C 206 " " NAG F 401 " - " ASN F 49 " " NAG F 402 " - " ASN F 54 " " NAG G 501 " - " ASN G 213 " " NAG G 502 " - " ASN G 186 " " NAG H 1 " - " ASN C 265 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 32 sheets defined 8.5% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.682A pdb=" N ILE C 106 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 107 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 192 removed outlier: 3.760A pdb=" N VAL C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.577A pdb=" N PHE C 260 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.767A pdb=" N ILE F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 192 removed outlier: 3.601A pdb=" N VAL F 192 " --> pdb=" O ARG F 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 192' Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 203 through 208 removed outlier: 3.807A pdb=" N TRP G 207 " --> pdb=" O ILE G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 removed outlier: 4.102A pdb=" N HIS G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 389 Processing helix chain 'G' and resid 403 through 405 No H-bonds generated for 'chain 'G' and resid 403 through 405' Processing helix chain 'G' and resid 426 through 431 removed outlier: 3.768A pdb=" N LEU G 431 " --> pdb=" O ARG G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.504A pdb=" N VAL B 45 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE A 133 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN B 50 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU A 135 " --> pdb=" O ASN B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 80 removed outlier: 3.675A pdb=" N LYS A 93 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 91 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 89 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.565A pdb=" N LEU A 122 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.580A pdb=" N GLY A 143 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN A 117 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A 141 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE A 119 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 139 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.513A pdb=" N VAL B 140 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.992A pdb=" N ARG C 34 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS C 148 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 94 " --> pdb=" O HIS C 148 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL C 150 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C 99 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP C 75 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.063A pdb=" N GLY C 111 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 125 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.063A pdb=" N GLY C 111 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.597A pdb=" N THR C 208 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 218 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 246 through 252 removed outlier: 3.990A pdb=" N PHE C 246 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.632A pdb=" N CYS D 99 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.539A pdb=" N ASN D 111 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS D 146 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL D 113 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS D 144 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN E 50 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS D 137 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS E 52 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N LEU D 139 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 45 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU E 135 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN D 48 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LYS E 137 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 138 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 115 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS E 144 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 113 " --> pdb=" O CYS E 144 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS E 146 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 111 " --> pdb=" O CYS E 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 74 through 78 Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 80 Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.713A pdb=" N SER F 55 " --> pdb=" O CYS F 126 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS F 126 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE F 129 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY F 111 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 178 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN F 176 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 84 removed outlier: 4.061A pdb=" N LEU F 76 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU F 97 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 78 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS F 95 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU F 80 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 93 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE F 82 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE F 91 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP F 98 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AC6, first strand: chain 'F' and resid 249 through 251 removed outlier: 3.638A pdb=" N HIS F 250 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE F 232 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 25 removed outlier: 5.564A pdb=" N LEU G 61 " --> pdb=" O HIS G 93 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N HIS G 93 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA G 91 " --> pdb=" O PRO G 63 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS G 65 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LEU G 82 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU G 164 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 84 " --> pdb=" O CYS G 162 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS G 162 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 86 " --> pdb=" O TYR G 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY G 156 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL G 92 " --> pdb=" O SER G 154 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER G 154 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.933A pdb=" N SER G 175 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 185 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 212 through 215 Processing sheet with id=AD1, first strand: chain 'G' and resid 250 through 255 removed outlier: 3.821A pdb=" N LEU G 254 " --> pdb=" O PHE G 233 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 233 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 273 " --> pdb=" O ILE G 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 305 through 307 removed outlier: 3.753A pdb=" N ARG G 305 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP G 317 " --> pdb=" O ARG G 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 338 through 340 Processing sheet with id=AD4, first strand: chain 'G' and resid 338 through 340 removed outlier: 3.597A pdb=" N GLU G 381 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 379 " --> pdb=" O VAL G 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 416 through 419 removed outlier: 4.589A pdb=" N LEU G 396 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY G 453 " --> pdb=" O ASP G 449 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP G 449 " --> pdb=" O GLY G 453 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU G 455 " --> pdb=" O LEU G 447 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3534 1.34 - 1.47: 2503 1.47 - 1.59: 4754 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 10878 Sorted by residual: bond pdb=" C VAL E 113 " pdb=" N PRO E 114 " ideal model delta sigma weight residual 1.333 1.358 -0.026 1.17e-02 7.31e+03 4.79e+00 bond pdb=" C ALA F 254 " pdb=" N PRO F 255 " ideal model delta sigma weight residual 1.333 1.357 -0.025 1.17e-02 7.31e+03 4.47e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CG PRO G 35 " pdb=" CD PRO G 35 " ideal model delta sigma weight residual 1.503 1.564 -0.061 3.40e-02 8.65e+02 3.25e+00 bond pdb=" C VAL F 151 " pdb=" N ASP F 152 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.47e-02 4.63e+03 2.51e+00 ... (remaining 10873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 14606 2.22 - 4.45: 229 4.45 - 6.67: 16 6.67 - 8.89: 4 8.89 - 11.12: 2 Bond angle restraints: 14857 Sorted by residual: angle pdb=" CB MET D 110 " pdb=" CG MET D 110 " pdb=" SD MET D 110 " ideal model delta sigma weight residual 112.70 123.82 -11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA GLN E 117 " pdb=" CB GLN E 117 " pdb=" CG GLN E 117 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB GLN E 117 " pdb=" CG GLN E 117 " pdb=" CD GLN E 117 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" CA GLN G 189 " pdb=" CB GLN G 189 " pdb=" CG GLN G 189 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB GLN G 189 " pdb=" CG GLN G 189 " pdb=" CD GLN G 189 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.70e+00 3.46e-01 1.10e+01 ... (remaining 14852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5897 18.00 - 36.00: 622 36.00 - 54.00: 177 54.00 - 72.00: 34 72.00 - 90.00: 19 Dihedral angle restraints: 6749 sinusoidal: 2850 harmonic: 3899 Sorted by residual: dihedral pdb=" CB CYS G 272 " pdb=" SG CYS G 272 " pdb=" SG CYS G 288 " pdb=" CB CYS G 288 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 50 " pdb=" CB CYS C 50 " ideal model delta sinusoidal sigma weight residual 93.00 167.62 -74.62 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS G 83 " pdb=" SG CYS G 83 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual -86.00 -150.42 64.42 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 6746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1436 0.061 - 0.122: 261 0.122 - 0.183: 11 0.183 - 0.245: 1 0.245 - 0.306: 1 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 265 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LEU G 262 " pdb=" N LEU G 262 " pdb=" C LEU G 262 " pdb=" CB LEU G 262 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" C2 NAG F 401 " pdb=" C1 NAG F 401 " pdb=" C3 NAG F 401 " pdb=" N2 NAG F 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1707 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 34 " 0.054 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO G 35 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 35 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 35 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 194 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 195 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 152 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO F 153 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 153 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 153 " -0.022 5.00e-02 4.00e+02 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 9397 3.22 - 3.78: 15943 3.78 - 4.34: 21052 4.34 - 4.90: 35265 Nonbonded interactions: 81896 Sorted by model distance: nonbonded pdb=" OG SER B 72 " pdb=" O CYS B 144 " model vdw 2.105 3.040 nonbonded pdb=" OG SER A 72 " pdb=" O CYS A 144 " model vdw 2.119 3.040 nonbonded pdb=" O SER F 72 " pdb=" NE2 GLN F 101 " model vdw 2.128 3.120 nonbonded pdb=" OG1 THR F 121 " pdb=" OE1 GLU F 123 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR F 99 " pdb=" O TRP F 142 " model vdw 2.170 3.040 ... (remaining 81891 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 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 45 or (resid 46 and (name N or name CA or nam \ e C or name O or name CB )) or resid 47 through 51 or resid 64 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 136 or (resid 137 and (name N or name CA or name C or name O \ or name CB )) or resid 138 through 150 or (resid 151 through 152 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 42 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 51 or resid 64 through 69 or (resi \ d 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throug \ h 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) or \ resid 109 through 127 or resid 130 through 152)) selection = (chain 'D' and (resid 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 127 or resid 130 through 136 or (resid 137 an \ d (name N or name CA or name C or name O or name CB )) or resid 138 through 150 \ or (resid 151 through 152 and (name N or name CA or name C or name O or name CB \ )))) } ncs_group { reference = (chain 'C' and (resid 33 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 or (resid 136 through 137 and (name N o \ r name CA or name C or name O or name CB )) or resid 138 through 139 or (resid 1 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 141 through \ 177 or (resid 178 and (name N or name CA or name C or name O or name CB )) or r \ esid 179 through 183 or (resid 184 and (name N or name CA or name C or name O or \ name CB )) or resid 185 through 190 or (resid 191 and (name N or name CA or nam \ e C or name O or name CB )) or resid 192 through 210 or resid 212 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 23 \ 4 or (resid 247 through 248 and (name N or name CA or name C or name O or name C \ B )) or resid 249 through 257 or (resid 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 268 or resid 281 through 298 or re \ sid 403 through 404)) selection = (chain 'F' and (resid 33 through 169 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 210 or resid 217 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.260 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 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 : 0.004 0.061 10910 Z= 0.183 Angle : 0.652 11.119 14932 Z= 0.334 Chirality : 0.045 0.306 1710 Planarity : 0.005 0.080 1917 Dihedral : 16.390 90.001 4114 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.21 % Allowed : 21.26 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.09 (0.23), residues: 1275 helix: -1.99 (0.59), residues: 73 sheet: -0.27 (0.25), residues: 461 loop : -0.84 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.016 0.002 TYR E 66 PHE 0.021 0.002 PHE F 286 TRP 0.015 0.001 TRP C 62 HIS 0.006 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00406 (10878) covalent geometry : angle 0.64072 (14857) SS BOND : bond 0.00494 ( 21) SS BOND : angle 1.62482 ( 42) hydrogen bonds : bond 0.29152 ( 283) hydrogen bonds : angle 11.49959 ( 765) link_BETA1-4 : bond 0.00550 ( 1) link_BETA1-4 : angle 1.80836 ( 3) link_NAG-ASN : bond 0.00430 ( 10) link_NAG-ASN : angle 1.99743 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7409 (t0) cc_final: 0.7151 (t0) REVERT: F 122 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7379 (m110) REVERT: F 154 ASP cc_start: 0.6493 (t0) cc_final: 0.6217 (t0) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.0950 time to fit residues: 24.9682 Evaluate side-chains 180 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 288 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.216377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.175293 restraints weight = 14448.452| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 2.94 r_work: 0.4238 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10910 Z= 0.177 Angle : 0.640 9.330 14932 Z= 0.328 Chirality : 0.045 0.232 1710 Planarity : 0.005 0.048 1917 Dihedral : 7.901 58.500 1669 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.44 % Allowed : 18.03 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.04 (0.23), residues: 1275 helix: -2.05 (0.57), residues: 75 sheet: -0.25 (0.24), residues: 490 loop : -0.80 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 123 TYR 0.017 0.002 TYR G 176 PHE 0.014 0.002 PHE D 133 TRP 0.016 0.002 TRP A 74 HIS 0.008 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00401 (10878) covalent geometry : angle 0.62620 (14857) SS BOND : bond 0.00391 ( 21) SS BOND : angle 1.58299 ( 42) hydrogen bonds : bond 0.04816 ( 283) hydrogen bonds : angle 8.70893 ( 765) link_BETA1-4 : bond 0.00476 ( 1) link_BETA1-4 : angle 1.22263 ( 3) link_NAG-ASN : bond 0.00449 ( 10) link_NAG-ASN : angle 2.48223 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.388 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: A 79 ASN cc_start: 0.7608 (t0) cc_final: 0.7380 (t0) REVERT: A 110 MET cc_start: 0.7265 (ttt) cc_final: 0.6946 (ttt) REVERT: D 81 ASP cc_start: 0.6481 (t0) cc_final: 0.6138 (t0) REVERT: F 45 GLN cc_start: 0.6461 (pt0) cc_final: 0.6244 (mt0) REVERT: F 120 ASN cc_start: 0.6826 (p0) cc_final: 0.6260 (m-40) REVERT: F 122 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7222 (m110) REVERT: F 154 ASP cc_start: 0.6451 (t0) cc_final: 0.6160 (t0) REVERT: F 262 GLN cc_start: 0.7204 (mp10) cc_final: 0.6956 (mm-40) REVERT: G 254 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7140 (pp) outliers start: 64 outliers final: 41 residues processed: 210 average time/residue: 0.0870 time to fit residues: 26.7827 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 176 GLN F 250 HIS F 297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.216960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.175930 restraints weight = 14387.794| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.94 r_work: 0.4249 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10910 Z= 0.150 Angle : 0.595 9.572 14932 Z= 0.301 Chirality : 0.045 0.238 1710 Planarity : 0.005 0.045 1917 Dihedral : 7.624 58.557 1662 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.36 % Allowed : 18.20 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.98 (0.23), residues: 1275 helix: -2.08 (0.57), residues: 75 sheet: -0.29 (0.23), residues: 502 loop : -0.68 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.016 0.001 TYR G 176 PHE 0.011 0.001 PHE D 133 TRP 0.014 0.002 TRP C 62 HIS 0.006 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00345 (10878) covalent geometry : angle 0.58421 (14857) SS BOND : bond 0.00311 ( 21) SS BOND : angle 1.43206 ( 42) hydrogen bonds : bond 0.03824 ( 283) hydrogen bonds : angle 7.83173 ( 765) link_BETA1-4 : bond 0.00484 ( 1) link_BETA1-4 : angle 1.33561 ( 3) link_NAG-ASN : bond 0.00427 ( 10) link_NAG-ASN : angle 2.02209 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.343 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: D 81 ASP cc_start: 0.6520 (t0) cc_final: 0.6127 (t0) REVERT: D 110 MET cc_start: 0.4025 (mmm) cc_final: 0.3361 (mmm) REVERT: F 120 ASN cc_start: 0.6769 (p0) cc_final: 0.6189 (m-40) REVERT: F 122 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7257 (m110) REVERT: F 154 ASP cc_start: 0.6469 (t0) cc_final: 0.6189 (t0) REVERT: F 259 GLU cc_start: 0.6590 (pm20) cc_final: 0.6383 (pm20) REVERT: F 262 GLN cc_start: 0.7203 (mp10) cc_final: 0.6950 (mm-40) REVERT: G 254 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7138 (pp) outliers start: 63 outliers final: 46 residues processed: 202 average time/residue: 0.0955 time to fit residues: 28.2298 Evaluate side-chains 204 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 128 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 148 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 = 0.4813 r_free = 0.4813 target = 0.216352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.175163 restraints weight = 14525.173| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.94 r_work: 0.4238 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10910 Z= 0.173 Angle : 0.610 9.487 14932 Z= 0.307 Chirality : 0.045 0.239 1710 Planarity : 0.005 0.048 1917 Dihedral : 7.453 59.826 1657 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.44 % Allowed : 18.54 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.03 (0.23), residues: 1275 helix: -1.93 (0.56), residues: 80 sheet: -0.34 (0.23), residues: 500 loop : -0.70 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.016 0.002 TYR G 176 PHE 0.012 0.002 PHE D 133 TRP 0.015 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00403 (10878) covalent geometry : angle 0.59910 (14857) SS BOND : bond 0.00396 ( 21) SS BOND : angle 1.55853 ( 42) hydrogen bonds : bond 0.03514 ( 283) hydrogen bonds : angle 7.57738 ( 765) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.31975 ( 3) link_NAG-ASN : bond 0.00400 ( 10) link_NAG-ASN : angle 1.97415 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.378 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: A 43 ARG cc_start: 0.6651 (mtp180) cc_final: 0.6432 (mtp85) REVERT: A 51 ILE cc_start: 0.3891 (OUTLIER) cc_final: 0.3432 (mt) REVERT: A 124 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6921 (mtp85) REVERT: B 146 CYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6381 (t) REVERT: C 190 MET cc_start: 0.6894 (mmt) cc_final: 0.5356 (mmt) REVERT: D 81 ASP cc_start: 0.6623 (t0) cc_final: 0.6234 (t0) REVERT: D 110 MET cc_start: 0.4404 (mmm) cc_final: 0.3737 (mmm) REVERT: F 122 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7251 (m110) REVERT: F 130 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7010 (tm-30) REVERT: F 259 GLU cc_start: 0.6641 (pm20) cc_final: 0.6435 (pm20) REVERT: F 262 GLN cc_start: 0.7225 (mp10) cc_final: 0.6947 (mm-40) REVERT: G 254 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7183 (pp) outliers start: 64 outliers final: 48 residues processed: 203 average time/residue: 0.0932 time to fit residues: 27.9128 Evaluate side-chains 206 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 113 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.0020 chunk 18 optimal weight: 0.5980 overall best weight: 0.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.226253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.191738 restraints weight = 15316.373| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 3.00 r_work: 0.4332 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10910 Z= 0.107 Angle : 0.566 9.453 14932 Z= 0.281 Chirality : 0.043 0.230 1710 Planarity : 0.004 0.056 1917 Dihedral : 6.808 56.025 1655 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.59 % Allowed : 19.64 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.88 (0.24), residues: 1275 helix: -1.89 (0.57), residues: 80 sheet: -0.25 (0.23), residues: 507 loop : -0.58 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.013 0.001 TYR A 66 PHE 0.009 0.001 PHE C 260 TRP 0.014 0.001 TRP B 74 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00253 (10878) covalent geometry : angle 0.55653 (14857) SS BOND : bond 0.00311 ( 21) SS BOND : angle 1.26759 ( 42) hydrogen bonds : bond 0.03030 ( 283) hydrogen bonds : angle 6.99182 ( 765) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 1.51426 ( 3) link_NAG-ASN : bond 0.00432 ( 10) link_NAG-ASN : angle 1.83742 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 0.389 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 51 ILE cc_start: 0.4099 (OUTLIER) cc_final: 0.3589 (mt) REVERT: D 81 ASP cc_start: 0.6721 (t0) cc_final: 0.6346 (t0) REVERT: D 110 MET cc_start: 0.4465 (mmm) cc_final: 0.3792 (mmm) REVERT: F 122 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7235 (m110) REVERT: F 130 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7255 (tm-30) REVERT: F 197 MET cc_start: 0.7470 (mtp) cc_final: 0.7238 (mtm) REVERT: F 259 GLU cc_start: 0.6595 (pm20) cc_final: 0.6395 (pm20) REVERT: G 178 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5662 (mp10) REVERT: G 254 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7114 (pp) outliers start: 54 outliers final: 36 residues processed: 194 average time/residue: 0.0959 time to fit residues: 27.1918 Evaluate side-chains 194 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.225507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.190635 restraints weight = 15428.601| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 3.01 r_work: 0.4317 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10910 Z= 0.119 Angle : 0.568 9.479 14932 Z= 0.281 Chirality : 0.044 0.231 1710 Planarity : 0.004 0.055 1917 Dihedral : 6.555 55.733 1652 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.93 % Allowed : 19.56 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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 (0.24), residues: 1275 helix: -1.84 (0.58), residues: 80 sheet: -0.17 (0.23), residues: 493 loop : -0.64 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.012 0.001 TYR G 176 PHE 0.009 0.001 PHE F 286 TRP 0.011 0.001 TRP B 74 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00284 (10878) covalent geometry : angle 0.55876 (14857) SS BOND : bond 0.00354 ( 21) SS BOND : angle 1.39345 ( 42) hydrogen bonds : bond 0.02921 ( 283) hydrogen bonds : angle 6.82419 ( 765) link_BETA1-4 : bond 0.00411 ( 1) link_BETA1-4 : angle 1.40121 ( 3) link_NAG-ASN : bond 0.00395 ( 10) link_NAG-ASN : angle 1.77699 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.381 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: A 51 ILE cc_start: 0.4125 (OUTLIER) cc_final: 0.3711 (mt) REVERT: A 79 ASN cc_start: 0.7893 (t0) cc_final: 0.7650 (t0) REVERT: A 84 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5703 (ttp80) REVERT: A 110 MET cc_start: 0.7332 (ttp) cc_final: 0.6898 (ttt) REVERT: A 124 ARG cc_start: 0.7393 (mtp85) cc_final: 0.7140 (mtp85) REVERT: D 81 ASP cc_start: 0.6772 (t0) cc_final: 0.6424 (t0) REVERT: D 110 MET cc_start: 0.4474 (mmm) cc_final: 0.4094 (mmm) REVERT: D 152 HIS cc_start: 0.5052 (OUTLIER) cc_final: 0.4334 (p-80) REVERT: E 62 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5905 (mmp-170) REVERT: F 122 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7324 (m110) REVERT: F 130 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7274 (tm-30) REVERT: F 197 MET cc_start: 0.7489 (mtp) cc_final: 0.7255 (mtm) REVERT: F 249 MET cc_start: 0.6589 (tpt) cc_final: 0.5690 (tpt) REVERT: F 259 GLU cc_start: 0.6566 (pm20) cc_final: 0.6364 (pm20) REVERT: G 178 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5720 (mp10) outliers start: 58 outliers final: 41 residues processed: 196 average time/residue: 0.0991 time to fit residues: 28.1310 Evaluate side-chains 200 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** 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 = 0.4806 r_free = 0.4806 target = 0.215762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.174705 restraints weight = 14341.504| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.93 r_work: 0.4227 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10910 Z= 0.195 Angle : 0.631 9.858 14932 Z= 0.314 Chirality : 0.046 0.248 1710 Planarity : 0.005 0.053 1917 Dihedral : 6.754 56.260 1651 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.10 % Allowed : 19.30 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.01 (0.23), residues: 1275 helix: -1.89 (0.57), residues: 80 sheet: -0.33 (0.23), residues: 497 loop : -0.70 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.014 0.002 TYR G 160 PHE 0.015 0.002 PHE F 82 TRP 0.017 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00454 (10878) covalent geometry : angle 0.62013 (14857) SS BOND : bond 0.00463 ( 21) SS BOND : angle 1.66589 ( 42) hydrogen bonds : bond 0.03202 ( 283) hydrogen bonds : angle 7.07981 ( 765) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 1.28150 ( 3) link_NAG-ASN : bond 0.00384 ( 10) link_NAG-ASN : angle 1.83906 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.464 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: A 51 ILE cc_start: 0.3877 (OUTLIER) cc_final: 0.3387 (mt) REVERT: A 84 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5539 (ttp80) REVERT: A 124 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6980 (mtp85) REVERT: C 190 MET cc_start: 0.6893 (mmt) cc_final: 0.5649 (mmt) REVERT: D 81 ASP cc_start: 0.6684 (t0) cc_final: 0.6333 (t0) REVERT: D 120 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7153 (mp) REVERT: E 62 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5976 (mmp-170) REVERT: F 122 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7425 (m110) REVERT: F 130 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7038 (tm-30) REVERT: G 254 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7216 (pp) outliers start: 60 outliers final: 46 residues processed: 194 average time/residue: 0.0978 time to fit residues: 27.6535 Evaluate side-chains 203 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN F 101 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 148 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 = 0.4879 r_free = 0.4879 target = 0.224630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.189739 restraints weight = 15151.700| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.95 r_work: 0.4310 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10910 Z= 0.125 Angle : 0.591 12.436 14932 Z= 0.289 Chirality : 0.044 0.235 1710 Planarity : 0.005 0.061 1917 Dihedral : 6.572 56.174 1651 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.10 % Allowed : 19.81 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.93 (0.24), residues: 1275 helix: -1.89 (0.57), residues: 80 sheet: -0.25 (0.23), residues: 494 loop : -0.65 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.013 0.001 TYR F 108 PHE 0.011 0.001 PHE C 260 TRP 0.014 0.001 TRP B 74 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00299 (10878) covalent geometry : angle 0.58167 (14857) SS BOND : bond 0.00336 ( 21) SS BOND : angle 1.39450 ( 42) hydrogen bonds : bond 0.02836 ( 283) hydrogen bonds : angle 6.76221 ( 765) link_BETA1-4 : bond 0.00376 ( 1) link_BETA1-4 : angle 1.41953 ( 3) link_NAG-ASN : bond 0.00387 ( 10) link_NAG-ASN : angle 1.76082 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.360 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: A 51 ILE cc_start: 0.4179 (OUTLIER) cc_final: 0.3756 (mt) REVERT: A 79 ASN cc_start: 0.7875 (t0) cc_final: 0.7620 (t0) REVERT: A 110 MET cc_start: 0.7286 (ttp) cc_final: 0.6927 (ttt) REVERT: A 124 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7172 (mtp85) REVERT: D 81 ASP cc_start: 0.6797 (t0) cc_final: 0.6486 (t0) REVERT: D 152 HIS cc_start: 0.4969 (OUTLIER) cc_final: 0.4157 (p-80) REVERT: E 62 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5876 (mmp-170) REVERT: F 122 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7355 (m110) REVERT: F 130 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7303 (tm-30) REVERT: F 197 MET cc_start: 0.7273 (mtp) cc_final: 0.7056 (mtm) REVERT: G 254 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7185 (pp) outliers start: 60 outliers final: 47 residues processed: 194 average time/residue: 0.0921 time to fit residues: 26.3216 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.215969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.174912 restraints weight = 14335.425| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.93 r_work: 0.4231 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10910 Z= 0.187 Angle : 0.636 11.945 14932 Z= 0.314 Chirality : 0.045 0.243 1710 Planarity : 0.005 0.060 1917 Dihedral : 6.740 56.146 1651 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.19 % Allowed : 19.73 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.02 (0.24), residues: 1275 helix: -1.94 (0.57), residues: 80 sheet: -0.38 (0.23), residues: 500 loop : -0.65 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.016 0.002 TYR G 160 PHE 0.014 0.002 PHE F 82 TRP 0.017 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00438 (10878) covalent geometry : angle 0.62617 (14857) SS BOND : bond 0.00433 ( 21) SS BOND : angle 1.62094 ( 42) hydrogen bonds : bond 0.03113 ( 283) hydrogen bonds : angle 6.92066 ( 765) link_BETA1-4 : bond 0.00316 ( 1) link_BETA1-4 : angle 1.30282 ( 3) link_NAG-ASN : bond 0.00374 ( 10) link_NAG-ASN : angle 1.79629 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.309 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: A 51 ILE cc_start: 0.3882 (OUTLIER) cc_final: 0.3385 (mt) REVERT: A 110 MET cc_start: 0.7250 (ttp) cc_final: 0.6958 (ttm) REVERT: A 124 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6926 (mtp85) REVERT: C 190 MET cc_start: 0.6874 (mmt) cc_final: 0.5597 (mmt) REVERT: D 81 ASP cc_start: 0.6704 (t0) cc_final: 0.6401 (t0) REVERT: D 152 HIS cc_start: 0.4782 (OUTLIER) cc_final: 0.4035 (p-80) REVERT: E 62 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.6007 (mmp-170) REVERT: E 66 TYR cc_start: 0.6840 (m-80) cc_final: 0.6524 (m-80) REVERT: F 122 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7343 (m110) REVERT: F 130 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7053 (tm-30) REVERT: G 178 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5995 (mm110) REVERT: G 254 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7238 (pp) outliers start: 61 outliers final: 50 residues processed: 197 average time/residue: 0.0942 time to fit residues: 27.0693 Evaluate side-chains 208 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.216045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.174975 restraints weight = 14233.092| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.92 r_work: 0.4232 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10910 Z= 0.184 Angle : 0.641 11.602 14932 Z= 0.317 Chirality : 0.045 0.241 1710 Planarity : 0.005 0.062 1917 Dihedral : 6.798 56.267 1651 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.68 % Allowed : 20.15 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -1.06 (0.24), residues: 1275 helix: -1.92 (0.57), residues: 80 sheet: -0.40 (0.23), residues: 487 loop : -0.70 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.015 0.002 TYR F 108 PHE 0.014 0.002 PHE C 260 TRP 0.017 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00430 (10878) covalent geometry : angle 0.63116 (14857) SS BOND : bond 0.00469 ( 21) SS BOND : angle 1.62587 ( 42) hydrogen bonds : bond 0.03084 ( 283) hydrogen bonds : angle 6.87540 ( 765) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 1.40532 ( 3) link_NAG-ASN : bond 0.00374 ( 10) link_NAG-ASN : angle 1.82891 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3989 (OUTLIER) cc_final: 0.3453 (mt) REVERT: A 110 MET cc_start: 0.7288 (ttp) cc_final: 0.6990 (ttm) REVERT: A 124 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6888 (mtp85) REVERT: C 190 MET cc_start: 0.6861 (mmt) cc_final: 0.5639 (mmt) REVERT: D 81 ASP cc_start: 0.6653 (t0) cc_final: 0.6343 (t0) REVERT: D 152 HIS cc_start: 0.4827 (OUTLIER) cc_final: 0.4037 (p-80) REVERT: E 62 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5981 (mmp-170) REVERT: F 122 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7378 (m110) REVERT: F 130 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7077 (tm-30) REVERT: G 164 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6973 (mm-30) REVERT: G 254 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7353 (pp) outliers start: 55 outliers final: 47 residues processed: 196 average time/residue: 0.0918 time to fit residues: 26.5317 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 50.0000 chunk 3 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.224709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.189844 restraints weight = 15297.934| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.97 r_work: 0.4322 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10910 Z= 0.126 Angle : 0.604 11.319 14932 Z= 0.296 Chirality : 0.044 0.230 1710 Planarity : 0.005 0.061 1917 Dihedral : 6.597 56.044 1651 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.76 % Allowed : 20.07 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.97 (0.24), residues: 1275 helix: -1.87 (0.57), residues: 80 sheet: -0.33 (0.23), residues: 486 loop : -0.64 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.014 0.002 TYR F 108 PHE 0.010 0.001 PHE C 260 TRP 0.015 0.001 TRP B 74 HIS 0.008 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00304 (10878) covalent geometry : angle 0.59492 (14857) SS BOND : bond 0.00322 ( 21) SS BOND : angle 1.41523 ( 42) hydrogen bonds : bond 0.02758 ( 283) hydrogen bonds : angle 6.55655 ( 765) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 1.47493 ( 3) link_NAG-ASN : bond 0.00461 ( 10) link_NAG-ASN : angle 1.73989 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4710.20 seconds wall clock time: 80 minutes 43.33 seconds (4843.33 seconds total)