Starting phenix.real_space_refine on Fri Feb 14 21:00:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwn_26837/02_2025/7uwn_26837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwn_26837/02_2025/7uwn_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_26837/02_2025/7uwn_26837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwn_26837/02_2025/7uwn_26837.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwn_26837/02_2025/7uwn_26837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwn_26837/02_2025/7uwn_26837.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG: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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 2} 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, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} 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: 6.46, per 1000 atoms: 0.61 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.74 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: 3.37 Time building geometry restraints manager: 2.76 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 298 or \ resid 401 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: 0.760 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.200 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- 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 10878 Z= 0.270 Angle : 0.641 11.119 14857 Z= 0.331 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (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 TRP 0.015 0.001 TRP C 62 HIS 0.006 0.001 HIS C 175 PHE 0.021 0.002 PHE F 286 TYR 0.016 0.002 TYR E 66 ARG 0.005 0.000 ARG D 78 *********************** 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 : 1.263 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: 0.2230 time to fit residues: 57.9704 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 : 1.257 ------------------------------------------------------------------------------- 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 109 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** 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 297 HIS G 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.214666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.173414 restraints weight = 14268.694| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.91 r_work: 0.4211 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10878 Z= 0.351 Angle : 0.672 9.389 14857 Z= 0.347 Chirality : 0.047 0.240 1710 Planarity : 0.006 0.052 1917 Dihedral : 8.092 58.094 1669 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 6.04 % Allowed : 17.60 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1275 helix: -2.09 (0.56), residues: 75 sheet: -0.42 (0.23), residues: 503 loop : -0.85 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 62 HIS 0.009 0.001 HIS C 175 PHE 0.017 0.002 PHE C 144 TYR 0.017 0.002 TYR G 176 ARG 0.004 0.001 ARG D 78 *********************** 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 233 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 1.142 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: 0.7649 (t0) cc_final: 0.7408 (t0) REVERT: B 66 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5322 (p90) REVERT: B 146 CYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6183 (t) REVERT: D 81 ASP cc_start: 0.6535 (t0) cc_final: 0.6207 (t0) REVERT: F 34 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: F 45 GLN cc_start: 0.6499 (pt0) cc_final: 0.6256 (mt0) REVERT: F 120 ASN cc_start: 0.6663 (p0) cc_final: 0.6194 (m-40) REVERT: F 122 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7270 (m110) REVERT: F 154 ASP cc_start: 0.6529 (t0) cc_final: 0.6220 (t0) REVERT: F 259 GLU cc_start: 0.6813 (pm20) cc_final: 0.6595 (pm20) REVERT: F 262 GLN cc_start: 0.7187 (mp10) cc_final: 0.6935 (mm-40) REVERT: G 254 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7253 (pp) outliers start: 71 outliers final: 42 residues processed: 216 average time/residue: 0.2127 time to fit residues: 66.9322 Evaluate side-chains 209 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER 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 66 TYR 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 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR 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 D residue 120 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 141 SER Chi-restraints excluded: chain F residue 34 ARG 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 222 THR 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 124 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 104 optimal weight: 0.0070 chunk 46 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 50.0000 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 176 GLN F 250 HIS G 370 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.216287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.175054 restraints weight = 14440.803| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.96 r_work: 0.4242 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10878 Z= 0.239 Angle : 0.597 9.448 14857 Z= 0.304 Chirality : 0.045 0.250 1710 Planarity : 0.005 0.047 1917 Dihedral : 7.696 56.643 1662 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.44 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1275 helix: -2.11 (0.56), residues: 75 sheet: -0.36 (0.23), residues: 502 loop : -0.72 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 62 HIS 0.006 0.001 HIS F 148 PHE 0.013 0.002 PHE D 133 TYR 0.016 0.001 TYR G 176 ARG 0.004 0.000 ARG A 95 *********************** 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 223 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 1.084 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: 0.3879 (OUTLIER) cc_final: 0.3401 (mt) REVERT: D 81 ASP cc_start: 0.6555 (t0) cc_final: 0.6129 (t0) REVERT: D 110 MET cc_start: 0.4133 (mmm) cc_final: 0.3451 (mmm) REVERT: F 120 ASN cc_start: 0.6408 (p0) cc_final: 0.5984 (m-40) REVERT: F 122 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7279 (m110) REVERT: F 154 ASP cc_start: 0.6559 (t0) cc_final: 0.6262 (t0) REVERT: F 259 GLU cc_start: 0.6822 (pm20) cc_final: 0.6512 (pm20) REVERT: F 262 GLN cc_start: 0.7200 (mp10) cc_final: 0.6938 (mm-40) REVERT: G 254 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7193 (pp) outliers start: 64 outliers final: 46 residues processed: 205 average time/residue: 0.2224 time to fit residues: 66.0461 Evaluate side-chains 207 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 93 LYS 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 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 235 THR 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 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 125 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.217349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.176444 restraints weight = 14358.056| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.94 r_work: 0.4252 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10878 Z= 0.211 Angle : 0.584 9.481 14857 Z= 0.294 Chirality : 0.044 0.236 1710 Planarity : 0.005 0.046 1917 Dihedral : 7.239 55.786 1656 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.53 % Allowed : 19.22 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1275 helix: -1.93 (0.56), residues: 80 sheet: -0.30 (0.23), residues: 498 loop : -0.66 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 74 HIS 0.006 0.001 HIS C 175 PHE 0.011 0.001 PHE F 144 TYR 0.015 0.001 TYR G 176 ARG 0.003 0.000 ARG F 263 *********************** 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 226 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3889 (OUTLIER) cc_final: 0.3411 (mt) REVERT: A 79 ASN cc_start: 0.7676 (t0) cc_final: 0.7379 (t0) REVERT: A 110 MET cc_start: 0.7001 (ttt) cc_final: 0.6725 (ttm) REVERT: D 81 ASP cc_start: 0.6572 (t0) cc_final: 0.6199 (t0) REVERT: D 110 MET cc_start: 0.4465 (mmm) cc_final: 0.3765 (mmm) REVERT: F 122 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7275 (m110) REVERT: F 259 GLU cc_start: 0.6836 (pm20) cc_final: 0.6604 (pm20) REVERT: F 262 GLN cc_start: 0.7270 (mp10) cc_final: 0.7012 (mm-40) REVERT: G 178 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: G 254 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7147 (pp) outliers start: 65 outliers final: 48 residues processed: 206 average time/residue: 0.2060 time to fit residues: 61.5481 Evaluate side-chains 211 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 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 116 VAL Chi-restraints excluded: chain C residue 127 VAL 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 47 VAL 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 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU 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 222 THR Chi-restraints excluded: chain F residue 261 HIS 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 203 ILE 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 88 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4810 r_free = 0.4810 target = 0.216169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.175206 restraints weight = 14319.127| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.92 r_work: 0.4232 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10878 Z= 0.264 Angle : 0.605 9.452 14857 Z= 0.305 Chirality : 0.045 0.241 1710 Planarity : 0.005 0.048 1917 Dihedral : 7.000 56.076 1653 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.38 % Allowed : 18.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1275 helix: -1.94 (0.56), residues: 80 sheet: -0.45 (0.23), residues: 503 loop : -0.70 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 PHE 0.011 0.002 PHE F 82 TYR 0.015 0.002 TYR G 176 ARG 0.003 0.000 ARG F 263 *********************** 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 226 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 151 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6633 (mtp180) cc_final: 0.6410 (mtp85) REVERT: A 51 ILE cc_start: 0.3897 (OUTLIER) cc_final: 0.3417 (mt) REVERT: A 84 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5571 (ttp80) REVERT: A 110 MET cc_start: 0.7046 (ttt) cc_final: 0.6791 (tpp) REVERT: A 124 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6995 (mtp85) REVERT: C 190 MET cc_start: 0.6879 (mmt) cc_final: 0.5589 (mmt) REVERT: D 81 ASP cc_start: 0.6662 (t0) cc_final: 0.6290 (t0) REVERT: D 110 MET cc_start: 0.4512 (mmm) cc_final: 0.4096 (mmm) REVERT: E 62 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5997 (mmp-170) REVERT: F 122 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7321 (m110) REVERT: F 130 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 259 GLU cc_start: 0.6864 (pm20) cc_final: 0.6624 (pm20) REVERT: F 262 GLN cc_start: 0.7281 (mp10) cc_final: 0.7058 (mm-40) REVERT: G 178 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5534 (mp10) REVERT: G 254 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7194 (pp) outliers start: 75 outliers final: 53 residues processed: 207 average time/residue: 0.2169 time to fit residues: 64.6524 Evaluate side-chains 208 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 84 ARG 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 A residue 154 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR 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 97 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 145 THR 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 47 VAL 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 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 182 VAL 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 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 203 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 117 optimal weight: 0.0020 chunk 45 optimal weight: 0.0020 chunk 122 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 126 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.217714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.176926 restraints weight = 14370.812| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 2.95 r_work: 0.4256 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10878 Z= 0.207 Angle : 0.575 9.430 14857 Z= 0.289 Chirality : 0.044 0.240 1710 Planarity : 0.005 0.054 1917 Dihedral : 6.831 56.341 1653 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.53 % Allowed : 19.81 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1275 helix: -1.90 (0.57), residues: 80 sheet: -0.29 (0.23), residues: 487 loop : -0.67 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.005 0.001 HIS C 175 PHE 0.011 0.001 PHE C 260 TYR 0.013 0.001 TYR G 176 ARG 0.002 0.000 ARG D 78 *********************** 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 217 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3870 (OUTLIER) cc_final: 0.3530 (mt) REVERT: A 84 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5478 (ttp80) REVERT: C 190 MET cc_start: 0.6797 (mmt) cc_final: 0.5521 (mmt) REVERT: D 81 ASP cc_start: 0.6623 (t0) cc_final: 0.6266 (t0) REVERT: D 110 MET cc_start: 0.4699 (mmm) cc_final: 0.4460 (mmm) REVERT: E 62 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5917 (mmp-170) REVERT: F 122 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7246 (m110) REVERT: F 130 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7018 (tm-30) REVERT: F 259 GLU cc_start: 0.6818 (pm20) cc_final: 0.6608 (pm20) REVERT: G 178 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5615 (mp10) REVERT: G 254 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7134 (pp) outliers start: 65 outliers final: 49 residues processed: 200 average time/residue: 0.2164 time to fit residues: 62.3262 Evaluate side-chains 206 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 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 47 VAL 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 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU 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 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 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 203 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 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** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4800 r_free = 0.4800 target = 0.215096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.173775 restraints weight = 14495.895| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.97 r_work: 0.4222 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10878 Z= 0.307 Angle : 0.620 9.679 14857 Z= 0.314 Chirality : 0.046 0.243 1710 Planarity : 0.005 0.052 1917 Dihedral : 7.013 56.435 1653 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.44 % Allowed : 19.56 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1275 helix: -1.94 (0.57), residues: 80 sheet: -0.49 (0.23), residues: 504 loop : -0.70 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 62 HIS 0.009 0.001 HIS F 138 PHE 0.016 0.002 PHE F 82 TYR 0.015 0.002 TYR G 176 ARG 0.003 0.000 ARG B 123 *********************** 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 215 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3883 (OUTLIER) cc_final: 0.3399 (mt) REVERT: A 84 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5579 (ttp80) REVERT: C 190 MET cc_start: 0.6925 (mmt) cc_final: 0.5643 (mmt) REVERT: D 81 ASP cc_start: 0.6674 (t0) cc_final: 0.6349 (t0) REVERT: D 110 MET cc_start: 0.4770 (mmm) cc_final: 0.4530 (mmm) REVERT: D 152 HIS cc_start: 0.4871 (OUTLIER) cc_final: 0.4209 (p-80) REVERT: E 62 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.6018 (mmp-170) REVERT: F 122 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7354 (m110) REVERT: F 130 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6999 (tm-30) REVERT: G 254 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7243 (pp) outliers start: 64 outliers final: 50 residues processed: 196 average time/residue: 0.2214 time to fit residues: 62.7231 Evaluate side-chains 204 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 110 MET 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 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 145 THR 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 260 PHE 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** C 155 GLN ** 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 = 0.4791 r_free = 0.4791 target = 0.214301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.173000 restraints weight = 14445.918| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.94 r_work: 0.4206 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10878 Z= 0.361 Angle : 0.663 10.981 14857 Z= 0.336 Chirality : 0.047 0.247 1710 Planarity : 0.005 0.058 1917 Dihedral : 7.146 56.387 1653 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.04 % Allowed : 19.73 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1275 helix: -1.98 (0.57), residues: 80 sheet: -0.56 (0.23), residues: 501 loop : -0.80 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 62 HIS 0.011 0.001 HIS F 138 PHE 0.019 0.002 PHE F 82 TYR 0.015 0.002 TYR F 108 ARG 0.004 0.000 ARG B 123 *********************** 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 223 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4003 (OUTLIER) cc_final: 0.3482 (mt) REVERT: C 143 ARG cc_start: 0.5780 (ttm-80) cc_final: 0.5558 (ttm-80) REVERT: C 190 MET cc_start: 0.6963 (mmt) cc_final: 0.5707 (mmt) REVERT: D 81 ASP cc_start: 0.6685 (t0) cc_final: 0.6359 (t0) REVERT: D 110 MET cc_start: 0.4917 (mmm) cc_final: 0.4687 (mmm) REVERT: D 120 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7134 (mp) REVERT: D 152 HIS cc_start: 0.4914 (OUTLIER) cc_final: 0.4213 (p-80) REVERT: E 62 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.6088 (mmp-170) REVERT: E 66 TYR cc_start: 0.6980 (m-80) cc_final: 0.6647 (m-80) REVERT: F 122 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7421 (m110) REVERT: F 130 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6993 (tm-30) REVERT: G 254 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7429 (pp) outliers start: 71 outliers final: 53 residues processed: 203 average time/residue: 0.2190 time to fit residues: 63.9733 Evaluate side-chains 210 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 138 ILE 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 71 THR 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 100 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 260 PHE 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 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 71 THR 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 56 THR Chi-restraints excluded: chain F residue 69 THR 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 261 HIS Chi-restraints excluded: chain F residue 262 GLN 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 96 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** C 155 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** G 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.215846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.174743 restraints weight = 14509.038| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.96 r_work: 0.4225 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10878 Z= 0.267 Angle : 0.625 11.589 14857 Z= 0.312 Chirality : 0.045 0.236 1710 Planarity : 0.005 0.063 1917 Dihedral : 6.996 56.481 1653 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.36 % Allowed : 20.66 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1275 helix: -1.95 (0.57), residues: 80 sheet: -0.49 (0.23), residues: 500 loop : -0.75 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 PHE 0.013 0.002 PHE C 260 TYR 0.015 0.002 TYR F 108 ARG 0.004 0.000 ARG A 69 *********************** 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 212 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.089 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: 0.3963 (OUTLIER) cc_final: 0.3410 (mt) REVERT: A 79 ASN cc_start: 0.7591 (t0) cc_final: 0.7285 (t0) REVERT: C 190 MET cc_start: 0.6896 (mmt) cc_final: 0.5650 (mmt) REVERT: D 81 ASP cc_start: 0.6683 (t0) cc_final: 0.6341 (t0) REVERT: D 152 HIS cc_start: 0.4863 (OUTLIER) cc_final: 0.4180 (p-80) REVERT: E 62 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.6028 (mmp-170) REVERT: E 66 TYR cc_start: 0.6863 (m-80) cc_final: 0.6585 (m-80) REVERT: F 122 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7369 (m110) REVERT: F 130 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7021 (tm-30) REVERT: G 67 GLN cc_start: 0.6938 (pt0) cc_final: 0.6510 (pt0) REVERT: G 254 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7366 (pp) outliers start: 63 outliers final: 50 residues processed: 196 average time/residue: 0.2032 time to fit residues: 58.0038 Evaluate side-chains 203 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 110 MET 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 A residue 154 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR 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 100 LEU 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 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 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 261 HIS 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 69 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.222861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.188208 restraints weight = 15216.264| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.90 r_work: 0.4295 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10878 Z= 0.250 Angle : 0.622 11.416 14857 Z= 0.308 Chirality : 0.045 0.232 1710 Planarity : 0.005 0.064 1917 Dihedral : 6.921 56.188 1653 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.68 % Allowed : 21.17 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1275 helix: -1.93 (0.57), residues: 80 sheet: -0.44 (0.24), residues: 487 loop : -0.71 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 62 HIS 0.009 0.001 HIS C 162 PHE 0.012 0.001 PHE C 260 TYR 0.014 0.002 TYR F 108 ARG 0.003 0.000 ARG A 84 ********************** 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 203 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 1.067 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: 0.4150 (OUTLIER) cc_final: 0.3541 (mt) REVERT: A 79 ASN cc_start: 0.7822 (t0) cc_final: 0.7533 (t0) REVERT: C 190 MET cc_start: 0.6965 (mmt) cc_final: 0.5665 (mmt) REVERT: D 81 ASP cc_start: 0.6807 (t0) cc_final: 0.6494 (t0) REVERT: D 152 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.4183 (p-80) REVERT: E 62 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.6038 (mmp-170) REVERT: E 66 TYR cc_start: 0.6879 (m-80) cc_final: 0.6649 (m-80) REVERT: F 122 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7420 (m110) REVERT: F 130 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7217 (tm-30) REVERT: G 67 GLN cc_start: 0.7238 (pt0) cc_final: 0.6963 (pt0) REVERT: G 254 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7391 (pp) outliers start: 55 outliers final: 49 residues processed: 188 average time/residue: 0.2152 time to fit residues: 58.8481 Evaluate side-chains 201 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 110 MET 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 A residue 154 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 71 THR 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 145 THR Chi-restraints excluded: chain C residue 202 LEU 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 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 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 261 HIS Chi-restraints excluded: chain F residue 262 GLN 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 122 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.223805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.189296 restraints weight = 15150.793| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.92 r_work: 0.4304 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10878 Z= 0.222 Angle : 0.602 11.630 14857 Z= 0.298 Chirality : 0.044 0.228 1710 Planarity : 0.005 0.064 1917 Dihedral : 6.793 56.206 1653 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.68 % Allowed : 21.26 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1275 helix: -1.89 (0.57), residues: 80 sheet: -0.37 (0.24), residues: 484 loop : -0.70 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 62 HIS 0.011 0.001 HIS C 162 PHE 0.010 0.001 PHE C 260 TYR 0.014 0.001 TYR F 108 ARG 0.003 0.000 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8993.88 seconds wall clock time: 158 minutes 40.77 seconds (9520.77 seconds total)