Starting phenix.real_space_refine on Mon Jul 28 19:51:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwn_26837/07_2025/7uwn_26837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwn_26837/07_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_26837/07_2025/7uwn_26837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwn_26837/07_2025/7uwn_26837.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwn_26837/07_2025/7uwn_26837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwn_26837/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.80, per 1000 atoms: 0.64 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 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: 1.79 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: 3.16 Time building geometry restraints manager: 3.09 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: 1.180 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 27.250 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10910 Z= 0.183 Angle : 0.652 11.119 14932 Z= 0.334 Chirality : 0.045 0.306 1710 Planarity : 0.005 0.080 1917 Dihedral : 16.390 90.001 4114 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.21 % Allowed : 21.26 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 10) link_NAG-ASN : angle 1.99743 ( 30) link_BETA1-4 : bond 0.00550 ( 1) link_BETA1-4 : angle 1.80836 ( 3) hydrogen bonds : bond 0.29152 ( 283) hydrogen bonds : angle 11.49959 ( 765) SS BOND : bond 0.00494 ( 21) SS BOND : angle 1.62482 ( 42) covalent geometry : bond 0.00406 (10878) covalent geometry : angle 0.64072 (14857) *********************** 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 : 1.232 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: 0.2194 time to fit residues: 57.3152 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 : 1.178 ------------------------------------------------------------------------------- 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 = 0.214667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.173390 restraints weight = 14268.779| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.91 r_work: 0.4212 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 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 10910 Z= 0.231 Angle : 0.687 9.389 14932 Z= 0.351 Chirality : 0.047 0.240 1710 Planarity : 0.006 0.052 1917 Dihedral : 8.092 58.096 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.58803 ( 30) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 1.17643 ( 3) hydrogen bonds : bond 0.04763 ( 283) hydrogen bonds : angle 8.73391 ( 765) SS BOND : bond 0.00609 ( 21) SS BOND : angle 1.77650 ( 42) covalent geometry : bond 0.00524 (10878) covalent geometry : angle 0.67182 (14857) *********************** 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 : 1.225 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: 0.7631 (t0) cc_final: 0.7401 (t0) REVERT: B 66 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5320 (p90) REVERT: B 146 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6146 (t) REVERT: D 81 ASP cc_start: 0.6541 (t0) cc_final: 0.6209 (t0) REVERT: F 34 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7706 (ptm160) REVERT: F 45 GLN cc_start: 0.6493 (pt0) cc_final: 0.6243 (mt0) REVERT: F 120 ASN cc_start: 0.6658 (p0) cc_final: 0.6191 (m-40) REVERT: F 122 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7265 (m110) REVERT: F 154 ASP cc_start: 0.6537 (t0) cc_final: 0.6226 (t0) REVERT: F 259 GLU cc_start: 0.6821 (pm20) cc_final: 0.6603 (pm20) REVERT: F 262 GLN cc_start: 0.7189 (mp10) cc_final: 0.6941 (mm-40) REVERT: G 254 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7259 (pp) outliers start: 71 outliers final: 42 residues processed: 216 average time/residue: 0.2023 time to fit residues: 63.7886 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 : 1.197 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 50.0000 chunk 73 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 176 GLN F 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.217183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.176162 restraints weight = 14465.001| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.95 r_work: 0.4261 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10910 Z= 0.140 Angle : 0.599 9.615 14932 Z= 0.301 Chirality : 0.044 0.239 1710 Planarity : 0.005 0.046 1917 Dihedral : 7.660 56.655 1662 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.44 % Allowed : 18.71 % Favored : 75.85 % 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: -1.02 (0.23), residues: 1275 helix: -2.09 (0.57), residues: 75 sheet: -0.32 (0.23), residues: 502 loop : -0.70 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 62 HIS 0.005 0.001 HIS C 175 PHE 0.011 0.001 PHE D 133 TYR 0.016 0.001 TYR G 176 ARG 0.004 0.000 ARG A 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 10) link_NAG-ASN : angle 2.24771 ( 30) link_BETA1-4 : bond 0.00481 ( 1) link_BETA1-4 : angle 1.38559 ( 3) hydrogen bonds : bond 0.03800 ( 283) hydrogen bonds : angle 7.84957 ( 765) SS BOND : bond 0.00342 ( 21) SS BOND : angle 1.32375 ( 42) covalent geometry : bond 0.00322 (10878) covalent geometry : angle 0.58696 (14857) *********************** 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 227 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.194 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: 0.3812 (OUTLIER) cc_final: 0.3341 (mt) REVERT: A 110 MET cc_start: 0.6916 (ttt) cc_final: 0.6693 (ttt) REVERT: B 146 CYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6248 (t) REVERT: D 81 ASP cc_start: 0.6527 (t0) cc_final: 0.6108 (t0) REVERT: D 110 MET cc_start: 0.4096 (mmm) cc_final: 0.3414 (mmm) REVERT: F 120 ASN cc_start: 0.6731 (p0) cc_final: 0.6196 (m-40) REVERT: F 122 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7223 (m110) REVERT: F 259 GLU cc_start: 0.6796 (pm20) cc_final: 0.6499 (pm20) REVERT: F 262 GLN cc_start: 0.7190 (mp10) cc_final: 0.6937 (mm-40) REVERT: G 254 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7161 (pp) outliers start: 64 outliers final: 46 residues processed: 208 average time/residue: 0.2044 time to fit residues: 62.0605 Evaluate side-chains 209 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 99 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 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 287 PHE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 32 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 37 optimal weight: 0.0570 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 GLN ** 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** G 67 GLN G 370 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.225084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.190469 restraints weight = 15252.671| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 2.95 r_work: 0.4325 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10910 Z= 0.114 Angle : 0.571 9.476 14932 Z= 0.285 Chirality : 0.044 0.236 1710 Planarity : 0.004 0.050 1917 Dihedral : 7.239 58.319 1657 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.51 % Allowed : 19.56 % Favored : 75.94 % 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: -0.89 (0.24), residues: 1275 helix: -1.87 (0.57), residues: 80 sheet: -0.26 (0.24), residues: 498 loop : -0.59 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 74 HIS 0.005 0.001 HIS C 175 PHE 0.009 0.001 PHE F 144 TYR 0.014 0.001 TYR G 176 ARG 0.003 0.000 ARG F 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 10) link_NAG-ASN : angle 2.14589 ( 30) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.40589 ( 3) hydrogen bonds : bond 0.03177 ( 283) hydrogen bonds : angle 7.32052 ( 765) SS BOND : bond 0.00312 ( 21) SS BOND : angle 1.39559 ( 42) covalent geometry : bond 0.00269 (10878) covalent geometry : angle 0.55946 (14857) *********************** 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 212 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7846 (t0) cc_final: 0.7584 (t0) REVERT: B 65 ASP cc_start: 0.6311 (m-30) cc_final: 0.6081 (m-30) REVERT: B 146 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6618 (t) REVERT: D 81 ASP cc_start: 0.6717 (t0) cc_final: 0.6318 (t0) REVERT: D 110 MET cc_start: 0.4455 (mmm) cc_final: 0.3761 (mmm) REVERT: F 122 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7259 (m110) REVERT: F 259 GLU cc_start: 0.6776 (pm20) cc_final: 0.6549 (pm20) REVERT: F 262 GLN cc_start: 0.7290 (mp10) cc_final: 0.7021 (mm-40) REVERT: G 178 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5616 (mp10) outliers start: 53 outliers final: 41 residues processed: 198 average time/residue: 0.2259 time to fit residues: 65.4110 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 99 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain E residue 67 TYR 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 122 ASN Chi-restraints excluded: chain F residue 124 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 102 optimal weight: 0.0870 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.225048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.190643 restraints weight = 15251.961| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.90 r_work: 0.4325 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10910 Z= 0.122 Angle : 0.571 9.465 14932 Z= 0.282 Chirality : 0.044 0.234 1710 Planarity : 0.004 0.051 1917 Dihedral : 6.791 55.973 1654 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.61 % Allowed : 18.96 % Favored : 75.43 % 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: -0.89 (0.24), residues: 1275 helix: -1.85 (0.57), residues: 80 sheet: -0.27 (0.23), residues: 506 loop : -0.59 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 448 HIS 0.005 0.001 HIS C 175 PHE 0.010 0.001 PHE C 180 TYR 0.015 0.001 TYR G 176 ARG 0.002 0.000 ARG F 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 10) link_NAG-ASN : angle 2.06427 ( 30) link_BETA1-4 : bond 0.00528 ( 1) link_BETA1-4 : angle 1.45180 ( 3) hydrogen bonds : bond 0.03024 ( 283) hydrogen bonds : angle 6.94880 ( 765) SS BOND : bond 0.00501 ( 21) SS BOND : angle 1.28898 ( 42) covalent geometry : bond 0.00286 (10878) covalent geometry : angle 0.56021 (14857) *********************** 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 220 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 1.119 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: 0.4250 (OUTLIER) cc_final: 0.3741 (mt) REVERT: A 79 ASN cc_start: 0.7874 (t0) cc_final: 0.7643 (t0) REVERT: A 84 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5634 (ttp80) REVERT: A 110 MET cc_start: 0.7249 (ttt) cc_final: 0.6900 (ttm) REVERT: A 124 ARG cc_start: 0.7358 (mtp85) cc_final: 0.7134 (mtp85) REVERT: D 78 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7838 (mtp180) REVERT: D 81 ASP cc_start: 0.6745 (t0) cc_final: 0.6378 (t0) REVERT: D 110 MET cc_start: 0.4429 (mmm) cc_final: 0.3773 (mmm) REVERT: F 122 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7273 (m110) REVERT: F 130 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7236 (tm-30) REVERT: F 259 GLU cc_start: 0.6808 (pm20) cc_final: 0.6593 (pm20) REVERT: G 178 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5628 (mp10) outliers start: 66 outliers final: 46 residues processed: 201 average time/residue: 0.2178 time to fit residues: 63.9732 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 97 GLU 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 E residue 67 TYR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 208 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 40.0000 chunk 4 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 115 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 0.0070 overall best weight: 2.3204 ------------------------------------------------------------------------------- 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 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.211033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.169499 restraints weight = 14353.943| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.93 r_work: 0.4163 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 10910 Z= 0.386 Angle : 0.814 12.631 14932 Z= 0.416 Chirality : 0.054 0.317 1710 Planarity : 0.006 0.060 1917 Dihedral : 7.473 56.385 1652 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.95 % Allowed : 19.73 % Favored : 74.32 % 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: -1.41 (0.23), residues: 1275 helix: -1.99 (0.57), residues: 79 sheet: -0.63 (0.22), residues: 522 loop : -0.98 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 62 HIS 0.012 0.002 HIS F 148 PHE 0.034 0.003 PHE C 144 TYR 0.018 0.003 TYR G 176 ARG 0.007 0.001 ARG B 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 10) link_NAG-ASN : angle 2.48955 ( 30) link_BETA1-4 : bond 0.00029 ( 1) link_BETA1-4 : angle 1.18336 ( 3) hydrogen bonds : bond 0.04347 ( 283) hydrogen bonds : angle 7.88712 ( 765) SS BOND : bond 0.00862 ( 21) SS BOND : angle 2.18824 ( 42) covalent geometry : bond 0.00881 (10878) covalent geometry : angle 0.79937 (14857) *********************** 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 231 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3716 (OUTLIER) cc_final: 0.3305 (mt) REVERT: A 79 ASN cc_start: 0.7639 (t0) cc_final: 0.7356 (t0) REVERT: A 124 ARG cc_start: 0.7317 (mtp85) cc_final: 0.7065 (mtp85) REVERT: B 65 ASP cc_start: 0.6494 (m-30) cc_final: 0.6202 (m-30) REVERT: C 190 MET cc_start: 0.7035 (mmt) cc_final: 0.5656 (mmt) REVERT: D 81 ASP cc_start: 0.6765 (t0) cc_final: 0.6381 (t0) REVERT: E 62 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6186 (mmp-170) REVERT: F 101 GLN cc_start: 0.7150 (mt0) cc_final: 0.6921 (mt0) REVERT: F 122 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7478 (m110) REVERT: F 130 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6980 (tm-30) REVERT: F 138 HIS cc_start: 0.5739 (OUTLIER) cc_final: 0.4478 (m90) REVERT: F 149 PHE cc_start: 0.7487 (m-80) cc_final: 0.5857 (m-80) REVERT: F 154 ASP cc_start: 0.6914 (t0) cc_final: 0.6571 (t0) REVERT: G 254 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7573 (pp) outliers start: 70 outliers final: 53 residues processed: 213 average time/residue: 0.2699 time to fit residues: 82.3203 Evaluate side-chains 217 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 66 TYR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET 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 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 120 LEU 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 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 138 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 106 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 126 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.216902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.175808 restraints weight = 14515.799| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.96 r_work: 0.4241 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10910 Z= 0.137 Angle : 0.629 12.195 14932 Z= 0.311 Chirality : 0.045 0.254 1710 Planarity : 0.005 0.058 1917 Dihedral : 6.928 56.991 1651 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.85 % Allowed : 20.92 % 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: -1.15 (0.23), residues: 1275 helix: -2.00 (0.56), residues: 80 sheet: -0.49 (0.23), residues: 500 loop : -0.73 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 62 HIS 0.006 0.001 HIS F 148 PHE 0.014 0.002 PHE C 260 TYR 0.016 0.002 TYR F 108 ARG 0.002 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 10) link_NAG-ASN : angle 2.17166 ( 30) link_BETA1-4 : bond 0.00520 ( 1) link_BETA1-4 : angle 1.57736 ( 3) hydrogen bonds : bond 0.03005 ( 283) hydrogen bonds : angle 7.14085 ( 765) SS BOND : bond 0.00536 ( 21) SS BOND : angle 1.63918 ( 42) covalent geometry : bond 0.00324 (10878) covalent geometry : angle 0.61668 (14857) *********************** 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 213 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 1.225 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: 0.3847 (OUTLIER) cc_final: 0.3430 (mt) REVERT: A 79 ASN cc_start: 0.7640 (t0) cc_final: 0.7336 (t0) REVERT: B 46 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6190 (mtm) REVERT: C 190 MET cc_start: 0.6803 (mmt) cc_final: 0.5603 (mmt) REVERT: D 81 ASP cc_start: 0.6632 (t0) cc_final: 0.6309 (t0) REVERT: D 152 HIS cc_start: 0.4813 (OUTLIER) cc_final: 0.4165 (p-80) REVERT: E 62 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5990 (mmp-170) REVERT: F 122 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7311 (m110) REVERT: F 130 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6986 (tm-30) REVERT: F 286 PHE cc_start: 0.7413 (m-10) cc_final: 0.7115 (m-10) REVERT: G 254 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7231 (pp) outliers start: 57 outliers final: 37 residues processed: 195 average time/residue: 0.2182 time to fit residues: 62.1364 Evaluate side-chains 197 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 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 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 65 ASP 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 96 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 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 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: 3.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 17 optimal weight: 0.3980 chunk 123 optimal weight: 8.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.214932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.173748 restraints weight = 14396.131| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.93 r_work: 0.4209 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10910 Z= 0.204 Angle : 0.658 11.929 14932 Z= 0.327 Chirality : 0.046 0.243 1710 Planarity : 0.005 0.056 1917 Dihedral : 7.010 56.143 1651 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.36 % Allowed : 20.49 % 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: -1.24 (0.23), residues: 1275 helix: -2.03 (0.56), 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 0.019 0.002 TRP F 62 HIS 0.007 0.001 HIS C 175 PHE 0.015 0.002 PHE F 82 TYR 0.016 0.002 TYR G 160 ARG 0.003 0.000 ARG B 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 10) link_NAG-ASN : angle 2.18513 ( 30) link_BETA1-4 : bond 0.00306 ( 1) link_BETA1-4 : angle 1.42311 ( 3) hydrogen bonds : bond 0.03236 ( 283) hydrogen bonds : angle 7.20395 ( 765) SS BOND : bond 0.00462 ( 21) SS BOND : angle 1.79787 ( 42) covalent geometry : bond 0.00477 (10878) covalent geometry : angle 0.64506 (14857) *********************** 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 211 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4026 (OUTLIER) cc_final: 0.3497 (mt) REVERT: D 81 ASP cc_start: 0.6691 (t0) cc_final: 0.6359 (t0) REVERT: D 152 HIS cc_start: 0.4858 (OUTLIER) cc_final: 0.4202 (p-80) REVERT: E 62 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6079 (mmp-170) REVERT: F 122 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7403 (m110) REVERT: F 130 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7009 (tm-30) REVERT: F 138 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.4550 (m90) REVERT: G 254 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7400 (pp) outliers start: 63 outliers final: 48 residues processed: 196 average time/residue: 0.2135 time to fit residues: 60.5920 Evaluate side-chains 202 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 71 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET 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 71 THR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 110 MET 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 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 138 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 50.0000 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** 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 = 0.4796 r_free = 0.4796 target = 0.214740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.173611 restraints weight = 14481.207| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.94 r_work: 0.4210 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10910 Z= 0.209 Angle : 0.675 11.792 14932 Z= 0.335 Chirality : 0.046 0.241 1710 Planarity : 0.005 0.060 1917 Dihedral : 7.064 56.854 1651 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 20.83 % Favored : 74.40 % 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: -2.03 (0.56), residues: 80 sheet: -0.47 (0.24), residues: 483 loop : -0.86 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 62 HIS 0.008 0.001 HIS C 175 PHE 0.016 0.002 PHE F 82 TYR 0.016 0.002 TYR F 108 ARG 0.003 0.000 ARG A 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 10) link_NAG-ASN : angle 2.18522 ( 30) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.43558 ( 3) hydrogen bonds : bond 0.03174 ( 283) hydrogen bonds : angle 7.19424 ( 765) SS BOND : bond 0.00447 ( 21) SS BOND : angle 1.86203 ( 42) covalent geometry : bond 0.00486 (10878) covalent geometry : angle 0.66159 (14857) *********************** 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: 56 poor density : 156 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4028 (OUTLIER) cc_final: 0.3469 (mt) REVERT: A 79 ASN cc_start: 0.7643 (t0) cc_final: 0.7323 (t0) REVERT: A 110 MET cc_start: 0.6997 (ttt) cc_final: 0.6696 (ttm) REVERT: C 190 MET cc_start: 0.6928 (mmt) cc_final: 0.5686 (mmt) REVERT: D 81 ASP cc_start: 0.6686 (t0) cc_final: 0.6359 (t0) REVERT: D 152 HIS cc_start: 0.4939 (OUTLIER) cc_final: 0.4223 (p-80) REVERT: E 62 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.6060 (mmp-170) REVERT: E 66 TYR cc_start: 0.6861 (m-80) cc_final: 0.6576 (m-80) REVERT: F 122 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7432 (m110) REVERT: F 130 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6986 (tm-30) REVERT: F 138 HIS cc_start: 0.5506 (OUTLIER) cc_final: 0.4426 (m90) REVERT: G 254 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7397 (pp) outliers start: 56 outliers final: 48 residues processed: 199 average time/residue: 0.2557 time to fit residues: 73.0282 Evaluate side-chains 207 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 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 71 THR Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 140 VAL 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 122 ASN Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 294 CYS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 288 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 162 HIS ** 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 ** 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 = 0.4822 r_free = 0.4822 target = 0.217268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.176584 restraints weight = 14376.465| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.94 r_work: 0.4250 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10910 Z= 0.136 Angle : 0.634 11.573 14932 Z= 0.312 Chirality : 0.044 0.227 1710 Planarity : 0.005 0.065 1917 Dihedral : 6.834 55.953 1651 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.42 % Allowed : 21.17 % Favored : 74.40 % 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 (0.24), residues: 1275 helix: -1.97 (0.57), residues: 80 sheet: -0.40 (0.24), residues: 484 loop : -0.75 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.009 0.001 HIS C 162 PHE 0.010 0.001 PHE C 260 TYR 0.016 0.002 TYR F 108 ARG 0.002 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 10) link_NAG-ASN : angle 2.10466 ( 30) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 1.55176 ( 3) hydrogen bonds : bond 0.02879 ( 283) hydrogen bonds : angle 6.80994 ( 765) SS BOND : bond 0.00307 ( 21) SS BOND : angle 1.57967 ( 42) covalent geometry : bond 0.00326 (10878) covalent geometry : angle 0.62202 (14857) ********************** 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 199 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.3956 (OUTLIER) cc_final: 0.3521 (mt) REVERT: A 79 ASN cc_start: 0.7626 (t0) cc_final: 0.7309 (t0) REVERT: A 110 MET cc_start: 0.6815 (ttt) cc_final: 0.6612 (tpp) REVERT: C 190 MET cc_start: 0.6824 (mmt) cc_final: 0.5635 (mmt) REVERT: D 81 ASP cc_start: 0.6600 (t0) cc_final: 0.6298 (t0) REVERT: D 152 HIS cc_start: 0.4946 (OUTLIER) cc_final: 0.4226 (p-80) REVERT: E 62 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5925 (mmp-170) REVERT: F 110 GLU cc_start: 0.6559 (pm20) cc_final: 0.5986 (pm20) REVERT: F 122 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7331 (m110) REVERT: F 130 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7001 (tm-30) REVERT: F 286 PHE cc_start: 0.7390 (m-80) cc_final: 0.7186 (m-10) REVERT: G 254 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7302 (pp) outliers start: 52 outliers final: 43 residues processed: 187 average time/residue: 0.2604 time to fit residues: 71.5600 Evaluate side-chains 195 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 104 optimal weight: 0.0370 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.220211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.180400 restraints weight = 14357.405| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.92 r_work: 0.4306 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10910 Z= 0.111 Angle : 0.600 11.248 14932 Z= 0.292 Chirality : 0.043 0.213 1710 Planarity : 0.005 0.065 1917 Dihedral : 6.515 57.326 1651 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.32 % Allowed : 22.53 % 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: -0.97 (0.24), residues: 1275 helix: -1.88 (0.57), residues: 80 sheet: -0.31 (0.24), residues: 495 loop : -0.65 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 74 HIS 0.009 0.001 HIS C 162 PHE 0.007 0.001 PHE F 286 TYR 0.012 0.001 TYR G 176 ARG 0.004 0.000 ARG F 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 10) link_NAG-ASN : angle 2.04044 ( 30) link_BETA1-4 : bond 0.00136 ( 1) link_BETA1-4 : angle 1.50802 ( 3) hydrogen bonds : bond 0.02627 ( 283) hydrogen bonds : angle 6.33618 ( 765) SS BOND : bond 0.00273 ( 21) SS BOND : angle 1.29378 ( 42) covalent geometry : bond 0.00270 (10878) covalent geometry : angle 0.59054 (14857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10217.09 seconds wall clock time: 178 minutes 56.09 seconds (10736.09 seconds total)