Starting phenix.real_space_refine on Sat Jul 4 06:08:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usf_26737/07_2026/7usf_26737.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 8 6.06 5 P 150 5.49 5 S 64 5.16 5 C 11632 2.51 5 N 3472 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2121 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain: "B" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2019 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Chain: "C" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1922 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1871 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 79.129 110.276 55.058 1.00101.43 S ATOM 320 SG CYS A 40 78.963 106.675 56.185 1.00103.87 S ATOM 2420 SG CYS B 37 14.537 81.224 45.444 1.00121.13 S ATOM 2441 SG CYS B 40 14.038 77.220 46.958 1.00123.63 S ATOM 4435 SG CYS C 37 40.874 151.914 71.798 1.00204.27 S ATOM 4456 SG CYS C 40 38.126 149.786 70.059 1.00204.91 S ATOM 6325 SG CYS D 37 50.304 127.400 26.565 1.00181.93 S ATOM 6346 SG CYS D 40 52.486 127.361 29.823 1.00187.21 S Restraints were copied for chains: E, F, G, H, L, M, N Time building chain proxies: 4.95, per 1000 atoms: 0.26 Number of scatterers: 18988 At special positions: 0 Unit cell: (140.17, 168.99, 115.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Ca 2 19.99 S 64 16.00 P 150 15.00 O 3660 8.00 N 3472 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 761.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 13 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 9 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 37 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" ND1 HIS D 13 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 9 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 37 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" ND1 HIS G 13 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 9 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 37 " pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" ND1 HIS H 13 " pdb="ZN ZN H 401 " - pdb=" NE2 HIS H 9 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 37 " Number of angles added : 14 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 45.9% alpha, 16.8% beta 72 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.578A pdb=" N CYS A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 6.761A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 175 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.538A pdb=" N LEU B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.706A pdb=" N CYS B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 152 through 172 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 70 through 75 removed outlier: 6.606A pdb=" N LYS C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 155 through 175 removed outlier: 4.581A pdb=" N LYS C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.503A pdb=" N GLU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 70 through 75 removed outlier: 6.714A pdb=" N LYS D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 155 through 171 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.578A pdb=" N CYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 removed outlier: 6.761A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 75 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 129 through 139 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 175 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.538A pdb=" N LEU F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.706A pdb=" N CYS F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 152 through 172 Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 202 through 209 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 70 through 75 removed outlier: 6.606A pdb=" N LYS G 74 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 114 Processing helix chain 'G' and resid 129 through 139 Processing helix chain 'G' and resid 155 through 175 removed outlier: 4.581A pdb=" N LYS G 173 " --> pdb=" O ASN G 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 194 Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.503A pdb=" N GLU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 70 through 75 removed outlier: 6.714A pdb=" N LYS H 74 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 129 through 139 Processing helix chain 'H' and resid 155 through 171 Processing helix chain 'H' and resid 179 through 194 Processing helix chain 'H' and resid 202 through 208 Processing sheet with id=1, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.762A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.753A pdb=" N CYS A 244 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 234 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 219 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.802A pdb=" N TYR B 77 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 65 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 120 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 144 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.627A pdb=" N THR B 237 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 246 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 235 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 262 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 89 through 94 removed outlier: 6.522A pdb=" N TRP C 62 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 119 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 254 through 257 removed outlier: 3.786A pdb=" N THR C 237 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE C 246 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU C 235 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 233 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 219 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 89 through 94 removed outlier: 3.608A pdb=" N TYR D 77 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 119 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 254 through 257 removed outlier: 6.728A pdb=" N PHE D 246 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 235 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 219 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 89 through 93 removed outlier: 3.762A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TRP E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.753A pdb=" N CYS E 244 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL E 234 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER E 228 " --> pdb=" O ASP E 223 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL E 219 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 89 through 94 removed outlier: 3.802A pdb=" N TYR F 77 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 65 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 120 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 144 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 254 through 257 removed outlier: 3.627A pdb=" N THR F 237 " --> pdb=" O CYS F 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 246 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG F 262 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 89 through 94 removed outlier: 6.522A pdb=" N TRP G 62 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE G 119 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 254 through 257 removed outlier: 3.786A pdb=" N THR G 237 " --> pdb=" O CYS G 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE G 246 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU G 235 " --> pdb=" O PHE G 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP G 233 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 219 " --> pdb=" O ASP G 233 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.608A pdb=" N TYR H 77 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE H 119 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.728A pdb=" N PHE H 246 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU H 235 " --> pdb=" O PHE H 246 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 219 " --> pdb=" O PRO H 232 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 190 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.40 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: 5270 1.34 - 1.45: 4410 1.45 - 1.57: 9746 1.57 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19826 Sorted by residual: bond pdb=" C3' DA M 20 " pdb=" C2' DA M 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA J 20 " pdb=" C2' DA J 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG N 10 " pdb=" C2' DG N 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DG K 10 " pdb=" C2' DG K 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DC M 27 " pdb=" C2' DC M 27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 ... (remaining 19821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27028 2.05 - 4.10: 536 4.10 - 6.15: 16 6.15 - 8.20: 2 8.20 - 10.25: 2 Bond angle restraints: 27584 Sorted by residual: angle pdb=" N3 DT M 31 " pdb=" C4 DT M 31 " pdb=" O4 DT M 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 32 " pdb=" C4 DT J 32 " pdb=" O4 DT J 32 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT M 32 " pdb=" C4 DT M 32 " pdb=" O4 DT M 32 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9380 17.97 - 35.93: 1096 35.93 - 53.90: 586 53.90 - 71.87: 160 71.87 - 89.83: 12 Dihedral angle restraints: 11234 sinusoidal: 5438 harmonic: 5796 Sorted by residual: dihedral pdb=" CA TRP H 139 " pdb=" C TRP H 139 " pdb=" N LYS H 140 " pdb=" CA LYS H 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP D 139 " pdb=" C TRP D 139 " pdb=" N LYS D 140 " pdb=" CA LYS D 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY B 209 " pdb=" C GLY B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 11231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1948 0.036 - 0.071: 748 0.071 - 0.107: 256 0.107 - 0.143: 44 0.143 - 0.178: 6 Chirality restraints: 3002 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA TRP D 139 " pdb=" N TRP D 139 " pdb=" C TRP D 139 " pdb=" CB TRP D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2999 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN G 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN G 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA G 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN C 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN C 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 139 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.29e+00 pdb=" CG TRP D 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 139 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 139 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 126 2.59 - 3.17: 15458 3.17 - 3.75: 32720 3.75 - 4.32: 43088 4.32 - 4.90: 68437 Nonbonded interactions: 159829 Sorted by model distance: nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.017 3.040 nonbonded pdb=" OG1 THR D 202 " pdb=" OE1 GLU D 205 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASP A 65 " pdb="CA CA A 501 " model vdw 2.209 2.510 nonbonded pdb=" OD1 ASP E 65 " pdb="CA CA E 501 " model vdw 2.209 2.510 nonbonded pdb=" OH TYR C 242 " pdb=" OP1 DG L 10 " model vdw 2.219 3.040 ... (remaining 159824 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.040 19858 Z= 0.310 Angle : 0.653 20.278 27598 Z= 0.442 Chirality : 0.042 0.178 3002 Planarity : 0.004 0.052 3000 Dihedral : 19.616 89.833 7458 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1936 helix: 1.58 (0.18), residues: 810 sheet: 0.37 (0.30), residues: 342 loop : -0.47 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.015 0.001 TYR H 127 PHE 0.018 0.001 PHE G 88 TRP 0.041 0.002 TRP D 139 HIS 0.012 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.31 (19826) covalent geometry : angle 0.60973 / 0.44 (27584) hydrogen bonds : bond 0.13779 / 9.59 ( 960) hydrogen bonds : angle 6.48990 / 4.72 ( 2588) metal coordination : bond 0.01488 / 0.88 ( 32) metal coordination : angle 10.38485 / 6.03 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8452 (mmm) cc_final: 0.8179 (mmm) REVERT: A 244 CYS cc_start: 0.8664 (t) cc_final: 0.8120 (t) REVERT: B 130 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7631 (mmp80) REVERT: B 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7891 (m-70) REVERT: B 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6994 (tpt) REVERT: B 242 TYR cc_start: 0.8140 (m-10) cc_final: 0.7904 (m-10) REVERT: B 254 ILE cc_start: 0.8544 (mt) cc_final: 0.8316 (tt) REVERT: C 64 MET cc_start: 0.7830 (ttp) cc_final: 0.7601 (ttm) REVERT: C 65 ASP cc_start: 0.8305 (t0) cc_final: 0.8025 (t0) REVERT: C 85 TYR cc_start: 0.7379 (t80) cc_final: 0.7020 (t80) REVERT: C 110 PHE cc_start: 0.8497 (m-10) cc_final: 0.7893 (m-10) REVERT: C 196 MET cc_start: 0.7994 (ptp) cc_final: 0.6728 (ptp) REVERT: C 205 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 7 GLU cc_start: 0.8884 (pt0) cc_final: 0.8365 (pp20) REVERT: D 62 TRP cc_start: 0.7266 (m-10) cc_final: 0.6954 (m-10) REVERT: D 134 GLU cc_start: 0.8224 (mp0) cc_final: 0.7979 (mp0) REVERT: D 138 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7062 (tpt-90) REVERT: D 159 ARG cc_start: 0.9011 (tmt-80) cc_final: 0.8572 (tpt90) REVERT: D 161 HIS cc_start: 0.7013 (m-70) cc_final: 0.6615 (m90) REVERT: D 196 MET cc_start: 0.7354 (mmm) cc_final: 0.6792 (mmm) REVERT: D 205 GLU cc_start: 0.8167 (mp0) cc_final: 0.7170 (mp0) REVERT: E 64 MET cc_start: 0.8792 (ttm) cc_final: 0.8592 (ttm) REVERT: E 218 MET cc_start: 0.8460 (mmm) cc_final: 0.8186 (mmm) REVERT: E 244 CYS cc_start: 0.8671 (t) cc_final: 0.8128 (t) REVERT: F 130 ARG cc_start: 0.7952 (mmp-170) cc_final: 0.7632 (mmp80) REVERT: F 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7890 (m-70) REVERT: F 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6992 (tpt) REVERT: F 242 TYR cc_start: 0.8139 (m-10) cc_final: 0.7899 (m-10) REVERT: F 254 ILE cc_start: 0.8547 (mt) cc_final: 0.8321 (tt) REVERT: G 64 MET cc_start: 0.7824 (ttp) cc_final: 0.7598 (ttm) REVERT: G 65 ASP cc_start: 0.8301 (t0) cc_final: 0.8016 (t0) REVERT: G 85 TYR cc_start: 0.7383 (t80) cc_final: 0.7019 (t80) REVERT: G 110 PHE cc_start: 0.8496 (m-10) cc_final: 0.7891 (m-10) REVERT: G 196 MET cc_start: 0.8001 (ptp) cc_final: 0.6738 (ptp) REVERT: G 205 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8671 (mt-10) REVERT: H 7 GLU cc_start: 0.8882 (pt0) cc_final: 0.8364 (pp20) REVERT: H 62 TRP cc_start: 0.7268 (m-10) cc_final: 0.6955 (m-10) REVERT: H 134 GLU cc_start: 0.8223 (mp0) cc_final: 0.7977 (mp0) REVERT: H 138 ARG cc_start: 0.7335 (ttt180) cc_final: 0.7065 (tpt-90) REVERT: H 159 ARG cc_start: 0.9012 (tmt-80) cc_final: 0.8575 (tpt90) REVERT: H 161 HIS cc_start: 0.7012 (m-70) cc_final: 0.6617 (m90) REVERT: H 196 MET cc_start: 0.7356 (mmm) cc_final: 0.6794 (mmm) REVERT: H 205 GLU cc_start: 0.8172 (mp0) cc_final: 0.7173 (mp0) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.1463 time to fit residues: 71.6515 Evaluate side-chains 208 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 192 ASN B 68 HIS C 12 HIS C 161 HIS C 192 ASN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 192 ASN F 68 HIS G 12 HIS G 161 HIS G 192 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.130458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093759 restraints weight = 39584.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092607 restraints weight = 21936.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092986 restraints weight = 16174.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093401 restraints weight = 13805.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.093624 restraints weight = 13010.261| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19858 Z= 0.203 Angle : 0.604 7.126 27598 Z= 0.336 Chirality : 0.042 0.173 3002 Planarity : 0.004 0.044 3000 Dihedral : 22.207 82.901 3740 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.90 % Allowed : 8.02 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1936 helix: 1.54 (0.18), residues: 828 sheet: 0.32 (0.29), residues: 354 loop : -0.48 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.020 0.002 TYR H 242 PHE 0.017 0.002 PHE C 189 TRP 0.012 0.001 TRP B 208 HIS 0.009 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (19826) covalent geometry : angle 0.60132 / 0.34 (27584) hydrogen bonds : bond 0.04542 / 3.13 ( 960) hydrogen bonds : angle 5.49771 / 3.99 ( 2588) metal coordination : bond 0.00860 / 0.59 ( 32) metal coordination : angle 2.58424 / 1.13 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 ARG cc_start: 0.7832 (mmp-170) cc_final: 0.7567 (mmp80) REVERT: B 134 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 201 HIS cc_start: 0.7780 (m-70) cc_final: 0.7443 (m-70) REVERT: B 220 MET cc_start: 0.7901 (tpt) cc_final: 0.7451 (tpt) REVERT: C 65 ASP cc_start: 0.8507 (t0) cc_final: 0.8271 (t0) REVERT: C 85 TYR cc_start: 0.7407 (t80) cc_final: 0.7073 (t80) REVERT: C 127 TYR cc_start: 0.6877 (m-10) cc_final: 0.6621 (m-10) REVERT: C 141 ILE cc_start: 0.8266 (mt) cc_final: 0.7991 (tt) REVERT: C 205 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8671 (mt-10) REVERT: D 7 GLU cc_start: 0.8796 (pt0) cc_final: 0.8500 (pm20) REVERT: D 134 GLU cc_start: 0.8434 (mp0) cc_final: 0.8039 (tm-30) REVERT: D 138 ARG cc_start: 0.7326 (ttt180) cc_final: 0.7064 (tpt-90) REVERT: D 161 HIS cc_start: 0.7343 (m-70) cc_final: 0.6960 (m90) REVERT: D 195 ASN cc_start: 0.8839 (m-40) cc_final: 0.8564 (t0) REVERT: D 196 MET cc_start: 0.7316 (mmm) cc_final: 0.6756 (mmm) REVERT: D 205 GLU cc_start: 0.8441 (mp0) cc_final: 0.7513 (mp0) REVERT: D 223 ASP cc_start: 0.8509 (t70) cc_final: 0.8130 (t0) REVERT: D 265 THR cc_start: 0.8239 (m) cc_final: 0.7772 (p) REVERT: D 269 GLU cc_start: 0.5691 (pt0) cc_final: 0.5334 (pt0) REVERT: F 130 ARG cc_start: 0.7821 (mmp-170) cc_final: 0.7558 (mmp80) REVERT: F 134 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7724 (tm-30) REVERT: F 201 HIS cc_start: 0.7771 (m-70) cc_final: 0.7435 (m-70) REVERT: F 220 MET cc_start: 0.7891 (tpt) cc_final: 0.7452 (tpt) REVERT: G 65 ASP cc_start: 0.8505 (t0) cc_final: 0.8272 (t0) REVERT: G 85 TYR cc_start: 0.7404 (t80) cc_final: 0.7066 (t80) REVERT: G 127 TYR cc_start: 0.6877 (m-10) cc_final: 0.6615 (m-10) REVERT: G 141 ILE cc_start: 0.8264 (mt) cc_final: 0.7992 (tt) REVERT: G 205 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8670 (mt-10) REVERT: H 7 GLU cc_start: 0.8794 (pt0) cc_final: 0.8497 (pm20) REVERT: H 134 GLU cc_start: 0.8439 (mp0) cc_final: 0.8040 (tm-30) REVERT: H 138 ARG cc_start: 0.7321 (ttt180) cc_final: 0.7060 (tpt-90) REVERT: H 161 HIS cc_start: 0.7344 (m-70) cc_final: 0.6963 (m90) REVERT: H 195 ASN cc_start: 0.8845 (m-40) cc_final: 0.8570 (t0) REVERT: H 196 MET cc_start: 0.7328 (mmm) cc_final: 0.6758 (mmm) REVERT: H 205 GLU cc_start: 0.8445 (mp0) cc_final: 0.7516 (mp0) REVERT: H 223 ASP cc_start: 0.8514 (t70) cc_final: 0.8126 (t0) REVERT: H 265 THR cc_start: 0.8245 (m) cc_final: 0.7775 (p) REVERT: H 269 GLU cc_start: 0.5693 (pt0) cc_final: 0.5339 (pt0) outliers start: 15 outliers final: 11 residues processed: 252 average time/residue: 0.1534 time to fit residues: 59.2688 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 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 = 0.4079 r_free = 0.4079 target = 0.130175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093476 restraints weight = 39706.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093656 restraints weight = 20809.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094012 restraints weight = 15884.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094578 restraints weight = 12704.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094465 restraints weight = 12106.738| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19858 Z= 0.149 Angle : 0.560 7.739 27598 Z= 0.313 Chirality : 0.040 0.194 3002 Planarity : 0.004 0.039 3000 Dihedral : 22.172 84.170 3740 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.27 % Allowed : 10.07 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1936 helix: 1.63 (0.18), residues: 814 sheet: 0.46 (0.29), residues: 366 loop : -0.43 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.016 0.001 TYR C 77 PHE 0.016 0.001 PHE C 23 TRP 0.015 0.001 TRP B 208 HIS 0.007 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (19826) covalent geometry : angle 0.55669 / 0.31 (27584) hydrogen bonds : bond 0.03950 / 2.73 ( 960) hydrogen bonds : angle 5.24052 / 3.78 ( 2588) metal coordination : bond 0.00492 / 0.34 ( 32) metal coordination : angle 2.69275 / 1.23 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.698 Fit side-chains REVERT: B 130 ARG cc_start: 0.7811 (mmp-170) cc_final: 0.7567 (mmp80) REVERT: B 134 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 201 HIS cc_start: 0.7681 (m-70) cc_final: 0.7375 (m-70) REVERT: B 220 MET cc_start: 0.7826 (tpt) cc_final: 0.7343 (tpt) REVERT: C 62 TRP cc_start: 0.7072 (m-10) cc_final: 0.6030 (m-10) REVERT: C 65 ASP cc_start: 0.8606 (t0) cc_final: 0.8334 (t0) REVERT: C 85 TYR cc_start: 0.7432 (t80) cc_final: 0.7186 (t80) REVERT: C 113 MET cc_start: 0.6712 (mtt) cc_final: 0.6441 (mtm) REVERT: C 192 ASN cc_start: 0.6133 (m-40) cc_final: 0.5754 (m110) REVERT: C 205 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 7 GLU cc_start: 0.8766 (pt0) cc_final: 0.8432 (pm20) REVERT: D 59 ARG cc_start: 0.7507 (mpp80) cc_final: 0.7033 (mpp80) REVERT: D 62 TRP cc_start: 0.7239 (m-10) cc_final: 0.6941 (m-10) REVERT: D 134 GLU cc_start: 0.8506 (mp0) cc_final: 0.8094 (tm-30) REVERT: D 161 HIS cc_start: 0.7430 (m-70) cc_final: 0.6803 (m90) REVERT: D 196 MET cc_start: 0.7283 (mmm) cc_final: 0.6511 (mmm) REVERT: D 205 GLU cc_start: 0.8425 (mp0) cc_final: 0.7548 (mp0) REVERT: D 220 MET cc_start: 0.9004 (mmm) cc_final: 0.8706 (mmm) REVERT: D 223 ASP cc_start: 0.8414 (t70) cc_final: 0.8119 (t0) REVERT: D 265 THR cc_start: 0.8142 (m) cc_final: 0.7742 (p) REVERT: D 269 GLU cc_start: 0.5702 (pt0) cc_final: 0.5338 (pt0) REVERT: F 130 ARG cc_start: 0.7801 (mmp-170) cc_final: 0.7562 (mmp80) REVERT: F 134 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7696 (tm-30) REVERT: F 201 HIS cc_start: 0.7678 (m-70) cc_final: 0.7373 (m-70) REVERT: F 220 MET cc_start: 0.7817 (tpt) cc_final: 0.7345 (tpt) REVERT: G 62 TRP cc_start: 0.7073 (m-10) cc_final: 0.6029 (m-10) REVERT: G 65 ASP cc_start: 0.8604 (t0) cc_final: 0.8333 (t0) REVERT: G 85 TYR cc_start: 0.7433 (t80) cc_final: 0.7180 (t80) REVERT: G 113 MET cc_start: 0.6709 (mtt) cc_final: 0.6438 (mtm) REVERT: G 192 ASN cc_start: 0.6119 (m-40) cc_final: 0.5742 (m110) REVERT: G 205 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8666 (mt-10) REVERT: H 7 GLU cc_start: 0.8763 (pt0) cc_final: 0.8429 (pm20) REVERT: H 59 ARG cc_start: 0.7501 (mpp80) cc_final: 0.7023 (mpp80) REVERT: H 62 TRP cc_start: 0.7243 (m-10) cc_final: 0.6944 (m-10) REVERT: H 134 GLU cc_start: 0.8513 (mp0) cc_final: 0.8097 (tm-30) REVERT: H 161 HIS cc_start: 0.7436 (m-70) cc_final: 0.6808 (m90) REVERT: H 196 MET cc_start: 0.7291 (mmm) cc_final: 0.6512 (mmm) REVERT: H 205 GLU cc_start: 0.8431 (mp0) cc_final: 0.7549 (mp0) REVERT: H 220 MET cc_start: 0.8996 (mmm) cc_final: 0.8705 (mmm) REVERT: H 223 ASP cc_start: 0.8417 (t70) cc_final: 0.8114 (t0) REVERT: H 265 THR cc_start: 0.8140 (m) cc_final: 0.7739 (p) REVERT: H 269 GLU cc_start: 0.5705 (pt0) cc_final: 0.5342 (pt0) outliers start: 21 outliers final: 11 residues processed: 244 average time/residue: 0.1477 time to fit residues: 56.3161 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 205 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN C 201 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN G 201 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.128310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.093246 restraints weight = 39610.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092048 restraints weight = 22526.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092553 restraints weight = 20165.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092917 restraints weight = 15431.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092980 restraints weight = 14262.322| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19858 Z= 0.193 Angle : 0.577 8.918 27598 Z= 0.321 Chirality : 0.041 0.197 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.295 84.331 3740 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.33 % Allowed : 11.10 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1936 helix: 1.63 (0.18), residues: 816 sheet: 0.46 (0.29), residues: 362 loop : -0.51 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 20 TYR 0.013 0.001 TYR D 242 PHE 0.013 0.001 PHE C 23 TRP 0.014 0.001 TRP B 208 HIS 0.006 0.001 HIS F 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (19826) covalent geometry : angle 0.57554 / 0.32 (27584) hydrogen bonds : bond 0.03996 / 2.78 ( 960) hydrogen bonds : angle 5.12313 / 3.68 ( 2588) metal coordination : bond 0.00773 / 0.53 ( 32) metal coordination : angle 1.66864 / 0.85 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.683 Fit side-chains REVERT: B 201 HIS cc_start: 0.7485 (m-70) cc_final: 0.7237 (m-70) REVERT: B 220 MET cc_start: 0.7765 (tpt) cc_final: 0.7436 (mmm) REVERT: C 62 TRP cc_start: 0.7229 (m-10) cc_final: 0.6191 (m-10) REVERT: C 65 ASP cc_start: 0.8592 (t0) cc_final: 0.8376 (t0) REVERT: C 113 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtm) REVERT: C 205 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 7 GLU cc_start: 0.8649 (pt0) cc_final: 0.8393 (pm20) REVERT: D 59 ARG cc_start: 0.7641 (mpp80) cc_final: 0.7186 (mpp80) REVERT: D 62 TRP cc_start: 0.7423 (m-10) cc_final: 0.7091 (m-10) REVERT: D 134 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: D 195 ASN cc_start: 0.8681 (m-40) cc_final: 0.8468 (t0) REVERT: D 196 MET cc_start: 0.7248 (mmm) cc_final: 0.6438 (mmm) REVERT: D 205 GLU cc_start: 0.8410 (mp0) cc_final: 0.7496 (mp0) REVERT: D 220 MET cc_start: 0.8939 (mmm) cc_final: 0.8680 (mmm) REVERT: D 265 THR cc_start: 0.8187 (m) cc_final: 0.7899 (p) REVERT: D 269 GLU cc_start: 0.6017 (pt0) cc_final: 0.5619 (pt0) REVERT: F 201 HIS cc_start: 0.7475 (m-70) cc_final: 0.7228 (m-70) REVERT: F 220 MET cc_start: 0.7751 (tpt) cc_final: 0.7436 (mmm) REVERT: G 62 TRP cc_start: 0.7227 (m-10) cc_final: 0.6200 (m-10) REVERT: G 65 ASP cc_start: 0.8598 (t0) cc_final: 0.8380 (t0) REVERT: G 113 MET cc_start: 0.6681 (mtt) cc_final: 0.6407 (mtm) REVERT: G 205 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8568 (mt-10) REVERT: H 7 GLU cc_start: 0.8641 (pt0) cc_final: 0.8386 (pm20) REVERT: H 59 ARG cc_start: 0.7643 (mpp80) cc_final: 0.7181 (mpp80) REVERT: H 62 TRP cc_start: 0.7434 (m-10) cc_final: 0.7101 (m-10) REVERT: H 134 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: H 195 ASN cc_start: 0.8695 (m-40) cc_final: 0.8475 (t0) REVERT: H 196 MET cc_start: 0.7265 (mmm) cc_final: 0.6446 (mmm) REVERT: H 205 GLU cc_start: 0.8414 (mp0) cc_final: 0.7492 (mp0) REVERT: H 220 MET cc_start: 0.8933 (mmm) cc_final: 0.8672 (mmm) REVERT: H 265 THR cc_start: 0.8193 (m) cc_final: 0.7903 (p) REVERT: H 269 GLU cc_start: 0.6021 (pt0) cc_final: 0.5623 (pt0) outliers start: 22 outliers final: 15 residues processed: 234 average time/residue: 0.1482 time to fit residues: 53.6307 Evaluate side-chains 213 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 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 = 0.4064 r_free = 0.4064 target = 0.128917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094663 restraints weight = 39324.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093949 restraints weight = 27817.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094373 restraints weight = 21949.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094709 restraints weight = 16627.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094905 restraints weight = 15199.084| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19858 Z= 0.151 Angle : 0.558 7.480 27598 Z= 0.311 Chirality : 0.040 0.173 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.249 85.178 3740 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.87 % Allowed : 11.76 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1936 helix: 1.58 (0.18), residues: 828 sheet: 0.45 (0.29), residues: 366 loop : -0.54 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 159 TYR 0.010 0.001 TYR F 177 PHE 0.012 0.001 PHE C 23 TRP 0.015 0.001 TRP F 208 HIS 0.005 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19826) covalent geometry : angle 0.55644 / 0.31 (27584) hydrogen bonds : bond 0.03685 / 2.56 ( 960) hydrogen bonds : angle 5.04414 / 3.62 ( 2588) metal coordination : bond 0.00575 / 0.40 ( 32) metal coordination : angle 2.14696 / 1.07 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7687 (tpt) cc_final: 0.7393 (mmm) REVERT: C 62 TRP cc_start: 0.7321 (m-10) cc_final: 0.6272 (m-10) REVERT: C 169 ASN cc_start: 0.6765 (m-40) cc_final: 0.5737 (t0) REVERT: C 205 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8491 (mt-10) REVERT: D 59 ARG cc_start: 0.7758 (mpp80) cc_final: 0.7282 (mpp80) REVERT: D 62 TRP cc_start: 0.7569 (m-10) cc_final: 0.7267 (m-10) REVERT: D 134 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: D 195 ASN cc_start: 0.8569 (m-40) cc_final: 0.8303 (t0) REVERT: D 196 MET cc_start: 0.7075 (mmm) cc_final: 0.6347 (mmm) REVERT: D 205 GLU cc_start: 0.8288 (mp0) cc_final: 0.7377 (mp0) REVERT: D 220 MET cc_start: 0.8841 (mmm) cc_final: 0.8562 (mmm) REVERT: D 251 GLU cc_start: 0.7686 (tp30) cc_final: 0.7329 (tp30) REVERT: D 265 THR cc_start: 0.8119 (m) cc_final: 0.7877 (p) REVERT: D 269 GLU cc_start: 0.6040 (pt0) cc_final: 0.5719 (pt0) REVERT: F 220 MET cc_start: 0.7680 (tpt) cc_final: 0.7389 (mmm) REVERT: G 62 TRP cc_start: 0.7321 (m-10) cc_final: 0.6274 (m-10) REVERT: G 169 ASN cc_start: 0.6768 (m-40) cc_final: 0.5741 (t0) REVERT: G 205 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8490 (mt-10) REVERT: H 59 ARG cc_start: 0.7759 (mpp80) cc_final: 0.7282 (mpp80) REVERT: H 62 TRP cc_start: 0.7570 (m-10) cc_final: 0.7266 (m-10) REVERT: H 134 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: H 195 ASN cc_start: 0.8575 (m-40) cc_final: 0.8309 (t0) REVERT: H 196 MET cc_start: 0.7085 (mmm) cc_final: 0.6346 (mmm) REVERT: H 205 GLU cc_start: 0.8290 (mp0) cc_final: 0.7375 (mp0) REVERT: H 220 MET cc_start: 0.8831 (mmm) cc_final: 0.8558 (mmm) REVERT: H 251 GLU cc_start: 0.7683 (tp30) cc_final: 0.7328 (tp30) REVERT: H 265 THR cc_start: 0.8114 (m) cc_final: 0.7873 (p) REVERT: H 269 GLU cc_start: 0.6035 (pt0) cc_final: 0.5712 (pt0) outliers start: 31 outliers final: 23 residues processed: 238 average time/residue: 0.1473 time to fit residues: 54.6604 Evaluate side-chains 225 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 178 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.4162 r_free = 0.4162 target = 0.132154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097917 restraints weight = 39036.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098699 restraints weight = 24679.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098829 restraints weight = 17921.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.099098 restraints weight = 14660.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099233 restraints weight = 13619.384| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19858 Z= 0.189 Angle : 0.584 6.263 27598 Z= 0.325 Chirality : 0.041 0.166 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.316 85.215 3740 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.87 % Allowed : 13.93 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1936 helix: 1.63 (0.19), residues: 818 sheet: 0.39 (0.28), residues: 374 loop : -0.52 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.013 0.001 TYR C 77 PHE 0.012 0.001 PHE C 23 TRP 0.015 0.001 TRP F 208 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (19826) covalent geometry : angle 0.58310 / 0.33 (27584) hydrogen bonds : bond 0.03828 / 2.66 ( 960) hydrogen bonds : angle 5.05494 / 3.62 ( 2588) metal coordination : bond 0.00828 / 0.56 ( 32) metal coordination : angle 1.77534 / 0.94 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TRP cc_start: 0.7238 (m-10) cc_final: 0.5678 (m-10) REVERT: C 113 MET cc_start: 0.6436 (mtm) cc_final: 0.5761 (mtp) REVERT: C 169 ASN cc_start: 0.6685 (m-40) cc_final: 0.5790 (t0) REVERT: C 205 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8444 (mt-10) REVERT: D 62 TRP cc_start: 0.7541 (m-10) cc_final: 0.7181 (m-10) REVERT: D 92 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7766 (p) REVERT: D 134 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: D 171 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8498 (mm) REVERT: D 195 ASN cc_start: 0.8583 (m-40) cc_final: 0.8333 (t0) REVERT: D 196 MET cc_start: 0.7016 (mmm) cc_final: 0.6523 (mmm) REVERT: D 205 GLU cc_start: 0.8313 (mp0) cc_final: 0.7604 (mp0) REVERT: D 220 MET cc_start: 0.8842 (mmm) cc_final: 0.8473 (mmm) REVERT: D 269 GLU cc_start: 0.6023 (pt0) cc_final: 0.5629 (pt0) REVERT: G 62 TRP cc_start: 0.7234 (m-10) cc_final: 0.5679 (m-10) REVERT: G 113 MET cc_start: 0.6435 (mtm) cc_final: 0.5748 (mtp) REVERT: G 169 ASN cc_start: 0.6690 (m-40) cc_final: 0.5793 (t0) REVERT: G 205 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8438 (mt-10) REVERT: H 62 TRP cc_start: 0.7535 (m-10) cc_final: 0.7174 (m-10) REVERT: H 92 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7765 (p) REVERT: H 134 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: H 171 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8498 (mm) REVERT: H 195 ASN cc_start: 0.8573 (m-40) cc_final: 0.8325 (t0) REVERT: H 196 MET cc_start: 0.7015 (mmm) cc_final: 0.6527 (mmm) REVERT: H 205 GLU cc_start: 0.8313 (mp0) cc_final: 0.7606 (mp0) REVERT: H 220 MET cc_start: 0.8835 (mmm) cc_final: 0.8467 (mmm) REVERT: H 269 GLU cc_start: 0.6028 (pt0) cc_final: 0.5631 (pt0) outliers start: 31 outliers final: 19 residues processed: 233 average time/residue: 0.1499 time to fit residues: 54.0939 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.131443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097318 restraints weight = 39303.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097264 restraints weight = 24866.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097491 restraints weight = 20148.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097756 restraints weight = 15427.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097966 restraints weight = 14037.070| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19858 Z= 0.200 Angle : 0.607 8.444 27598 Z= 0.336 Chirality : 0.041 0.159 3002 Planarity : 0.004 0.040 3000 Dihedral : 22.389 86.310 3740 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 14.78 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1936 helix: 1.56 (0.19), residues: 820 sheet: 0.37 (0.30), residues: 352 loop : -0.58 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 159 TYR 0.020 0.002 TYR A 77 PHE 0.012 0.001 PHE B 88 TRP 0.018 0.001 TRP G 255 HIS 0.006 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (19826) covalent geometry : angle 0.60612 / 0.34 (27584) hydrogen bonds : bond 0.03871 / 2.70 ( 960) hydrogen bonds : angle 5.06346 / 3.62 ( 2588) metal coordination : bond 0.00949 / 0.65 ( 32) metal coordination : angle 1.88780 / 1.05 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.729 Fit side-chains REVERT: C 62 TRP cc_start: 0.7171 (m-10) cc_final: 0.6728 (m-10) REVERT: C 113 MET cc_start: 0.6449 (mtm) cc_final: 0.5944 (mtp) REVERT: C 169 ASN cc_start: 0.6789 (m-40) cc_final: 0.5874 (t0) REVERT: C 205 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8520 (mt-10) REVERT: D 59 ARG cc_start: 0.7744 (mpp80) cc_final: 0.7406 (mpp80) REVERT: D 92 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7675 (p) REVERT: D 134 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: D 171 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 195 ASN cc_start: 0.8730 (m-40) cc_final: 0.8501 (t0) REVERT: D 196 MET cc_start: 0.7159 (mmm) cc_final: 0.6594 (mmm) REVERT: D 205 GLU cc_start: 0.8356 (mp0) cc_final: 0.7608 (mp0) REVERT: D 220 MET cc_start: 0.8871 (mmm) cc_final: 0.8384 (mmm) REVERT: D 251 GLU cc_start: 0.7697 (tp30) cc_final: 0.7492 (tp30) REVERT: D 269 GLU cc_start: 0.6088 (pt0) cc_final: 0.5723 (pt0) REVERT: G 62 TRP cc_start: 0.7163 (m-10) cc_final: 0.6723 (m-10) REVERT: G 113 MET cc_start: 0.6448 (mtm) cc_final: 0.5939 (mtp) REVERT: G 169 ASN cc_start: 0.6790 (m-40) cc_final: 0.5874 (t0) REVERT: G 205 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8522 (mt-10) REVERT: H 59 ARG cc_start: 0.7743 (mpp80) cc_final: 0.7408 (mpp80) REVERT: H 92 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7667 (p) REVERT: H 134 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: H 171 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8585 (mm) REVERT: H 195 ASN cc_start: 0.8726 (m-40) cc_final: 0.8499 (t0) REVERT: H 196 MET cc_start: 0.7161 (mmm) cc_final: 0.6596 (mmm) REVERT: H 205 GLU cc_start: 0.8359 (mp0) cc_final: 0.7610 (mp0) REVERT: H 220 MET cc_start: 0.8868 (mmm) cc_final: 0.8381 (mmm) REVERT: H 251 GLU cc_start: 0.7694 (tp30) cc_final: 0.7488 (tp30) REVERT: H 269 GLU cc_start: 0.6097 (pt0) cc_final: 0.5729 (pt0) outliers start: 37 outliers final: 22 residues processed: 243 average time/residue: 0.1483 time to fit residues: 55.9425 Evaluate side-chains 232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 153 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.130527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096467 restraints weight = 39307.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096279 restraints weight = 25133.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096512 restraints weight = 20776.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096779 restraints weight = 15760.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097006 restraints weight = 14323.414| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19858 Z= 0.237 Angle : 0.655 12.284 27598 Z= 0.354 Chirality : 0.043 0.167 3002 Planarity : 0.004 0.043 3000 Dihedral : 22.481 86.908 3740 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.81 % Allowed : 15.92 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1936 helix: 1.50 (0.19), residues: 820 sheet: 0.32 (0.29), residues: 360 loop : -0.61 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 159 TYR 0.019 0.002 TYR A 77 PHE 0.015 0.001 PHE B 88 TRP 0.017 0.001 TRP A 208 HIS 0.007 0.001 HIS F 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (19826) covalent geometry : angle 0.65374 / 0.35 (27584) hydrogen bonds : bond 0.04043 / 2.81 ( 960) hydrogen bonds : angle 5.11803 / 3.67 ( 2588) metal coordination : bond 0.01250 / 0.86 ( 32) metal coordination : angle 1.85223 / 1.12 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 TRP cc_start: 0.7133 (m-10) cc_final: 0.6698 (m-10) REVERT: C 113 MET cc_start: 0.6594 (mtm) cc_final: 0.6088 (mtp) REVERT: C 169 ASN cc_start: 0.6736 (m-40) cc_final: 0.5872 (t0) REVERT: C 205 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8526 (mt-10) REVERT: D 59 ARG cc_start: 0.7789 (mpp80) cc_final: 0.7429 (mpp80) REVERT: D 92 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7698 (p) REVERT: D 134 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: D 171 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8688 (mm) REVERT: D 195 ASN cc_start: 0.8690 (m-40) cc_final: 0.8463 (t0) REVERT: D 196 MET cc_start: 0.7165 (mmm) cc_final: 0.6795 (mmm) REVERT: D 205 GLU cc_start: 0.8431 (mp0) cc_final: 0.7971 (mp0) REVERT: D 220 MET cc_start: 0.8867 (mmm) cc_final: 0.8317 (mmm) REVERT: D 269 GLU cc_start: 0.6131 (pt0) cc_final: 0.5785 (pt0) REVERT: G 62 TRP cc_start: 0.7117 (m-10) cc_final: 0.6686 (m-10) REVERT: G 113 MET cc_start: 0.6589 (mtm) cc_final: 0.6084 (mtp) REVERT: G 169 ASN cc_start: 0.6743 (m-40) cc_final: 0.5876 (t0) REVERT: G 205 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8523 (mt-10) REVERT: H 59 ARG cc_start: 0.7786 (mpp80) cc_final: 0.7425 (mpp80) REVERT: H 92 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (p) REVERT: H 134 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: H 171 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8685 (mm) REVERT: H 195 ASN cc_start: 0.8691 (m-40) cc_final: 0.8460 (t0) REVERT: H 196 MET cc_start: 0.7171 (mmm) cc_final: 0.6794 (mmm) REVERT: H 205 GLU cc_start: 0.8432 (mp0) cc_final: 0.7970 (mp0) REVERT: H 220 MET cc_start: 0.8862 (mmm) cc_final: 0.8318 (mmm) REVERT: H 269 GLU cc_start: 0.6139 (pt0) cc_final: 0.5792 (pt0) outliers start: 30 outliers final: 20 residues processed: 234 average time/residue: 0.1516 time to fit residues: 55.1177 Evaluate side-chains 232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 HIS ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.132672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098816 restraints weight = 38811.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100399 restraints weight = 24136.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100367 restraints weight = 16618.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.100567 restraints weight = 13282.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100615 restraints weight = 12380.578| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19858 Z= 0.140 Angle : 0.602 8.002 27598 Z= 0.331 Chirality : 0.040 0.147 3002 Planarity : 0.004 0.049 3000 Dihedral : 22.336 86.998 3740 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.51 % Allowed : 16.89 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1936 helix: 1.61 (0.19), residues: 818 sheet: 0.29 (0.29), residues: 376 loop : -0.47 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 159 TYR 0.013 0.001 TYR E 77 PHE 0.013 0.001 PHE C 23 TRP 0.020 0.001 TRP A 208 HIS 0.005 0.001 HIS F 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (19826) covalent geometry : angle 0.59905 / 0.33 (27584) hydrogen bonds : bond 0.03526 / 2.44 ( 960) hydrogen bonds : angle 5.00513 / 3.59 ( 2588) metal coordination : bond 0.00803 / 0.56 ( 32) metal coordination : angle 2.48763 / 1.28 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8649 (tp) cc_final: 0.8428 (tp) REVERT: B 220 MET cc_start: 0.7724 (mmm) cc_final: 0.7502 (mmm) REVERT: C 62 TRP cc_start: 0.7034 (m-10) cc_final: 0.6640 (m-10) REVERT: C 113 MET cc_start: 0.6424 (mtm) cc_final: 0.5968 (mtp) REVERT: C 169 ASN cc_start: 0.6549 (m-40) cc_final: 0.5829 (t0) REVERT: C 205 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8443 (mt-10) REVERT: D 62 TRP cc_start: 0.7588 (m-10) cc_final: 0.7196 (m-10) REVERT: D 134 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: D 171 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8564 (mm) REVERT: D 195 ASN cc_start: 0.8645 (m-40) cc_final: 0.8364 (t0) REVERT: D 196 MET cc_start: 0.6841 (mmm) cc_final: 0.6580 (mmt) REVERT: D 205 GLU cc_start: 0.8517 (mp0) cc_final: 0.7909 (mp0) REVERT: D 220 MET cc_start: 0.8800 (mmm) cc_final: 0.8304 (mmm) REVERT: D 269 GLU cc_start: 0.6048 (pt0) cc_final: 0.5679 (pt0) REVERT: E 2 LEU cc_start: 0.8651 (tp) cc_final: 0.8428 (tp) REVERT: F 220 MET cc_start: 0.7737 (mmm) cc_final: 0.7518 (mmm) REVERT: G 62 TRP cc_start: 0.7038 (m-10) cc_final: 0.6644 (m-10) REVERT: G 113 MET cc_start: 0.6411 (mtm) cc_final: 0.5959 (mtp) REVERT: G 169 ASN cc_start: 0.6555 (m-40) cc_final: 0.5833 (t0) REVERT: G 205 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8439 (mt-10) REVERT: H 62 TRP cc_start: 0.7586 (m-10) cc_final: 0.7190 (m-10) REVERT: H 134 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: H 171 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8561 (mm) REVERT: H 195 ASN cc_start: 0.8638 (m-40) cc_final: 0.8371 (t0) REVERT: H 196 MET cc_start: 0.6831 (mmm) cc_final: 0.6571 (mmt) REVERT: H 205 GLU cc_start: 0.8517 (mp0) cc_final: 0.7911 (mp0) REVERT: H 220 MET cc_start: 0.8798 (mmm) cc_final: 0.8301 (mmm) REVERT: H 269 GLU cc_start: 0.6053 (pt0) cc_final: 0.5687 (pt0) outliers start: 25 outliers final: 15 residues processed: 235 average time/residue: 0.1439 time to fit residues: 52.7568 Evaluate side-chains 219 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 94 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.4173 r_free = 0.4173 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098978 restraints weight = 39191.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099660 restraints weight = 24182.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.099808 restraints weight = 18163.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.100085 restraints weight = 14487.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100250 restraints weight = 13465.048| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19858 Z= 0.141 Angle : 0.598 7.948 27598 Z= 0.328 Chirality : 0.040 0.147 3002 Planarity : 0.004 0.046 3000 Dihedral : 22.337 84.345 3740 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 17.01 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1936 helix: 1.62 (0.19), residues: 818 sheet: 0.10 (0.28), residues: 382 loop : -0.50 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 159 TYR 0.012 0.001 TYR A 77 PHE 0.013 0.001 PHE C 23 TRP 0.022 0.001 TRP A 208 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19826) covalent geometry : angle 0.59600 / 0.33 (27584) hydrogen bonds : bond 0.03447 / 2.39 ( 960) hydrogen bonds : angle 4.92710 / 3.54 ( 2588) metal coordination : bond 0.00621 / 0.43 ( 32) metal coordination : angle 2.24904 / 1.17 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8641 (tp) cc_final: 0.8401 (tp) REVERT: C 62 TRP cc_start: 0.6992 (m-10) cc_final: 0.6599 (m-10) REVERT: C 85 TYR cc_start: 0.6852 (t80) cc_final: 0.6436 (t80) REVERT: C 113 MET cc_start: 0.6420 (mtm) cc_final: 0.5972 (mtp) REVERT: C 169 ASN cc_start: 0.6500 (m-40) cc_final: 0.5841 (t0) REVERT: C 205 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 134 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: D 171 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8550 (mm) REVERT: D 195 ASN cc_start: 0.8652 (m-40) cc_final: 0.8362 (t0) REVERT: D 205 GLU cc_start: 0.8506 (mp0) cc_final: 0.7859 (mp0) REVERT: D 220 MET cc_start: 0.8769 (mmm) cc_final: 0.8271 (mmm) REVERT: D 269 GLU cc_start: 0.6033 (pt0) cc_final: 0.5669 (pt0) REVERT: E 2 LEU cc_start: 0.8643 (tp) cc_final: 0.8401 (tp) REVERT: G 62 TRP cc_start: 0.6992 (m-10) cc_final: 0.6602 (m-10) REVERT: G 85 TYR cc_start: 0.6844 (t80) cc_final: 0.6430 (t80) REVERT: G 113 MET cc_start: 0.6403 (mtm) cc_final: 0.5958 (mtp) REVERT: G 169 ASN cc_start: 0.6502 (m-40) cc_final: 0.5845 (t0) REVERT: G 205 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8431 (mt-10) REVERT: H 134 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: H 171 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8546 (mm) REVERT: H 195 ASN cc_start: 0.8649 (m-40) cc_final: 0.8373 (t0) REVERT: H 205 GLU cc_start: 0.8507 (mp0) cc_final: 0.7859 (mp0) REVERT: H 220 MET cc_start: 0.8767 (mmm) cc_final: 0.8265 (mmm) REVERT: H 269 GLU cc_start: 0.6035 (pt0) cc_final: 0.5669 (pt0) outliers start: 22 outliers final: 18 residues processed: 226 average time/residue: 0.1507 time to fit residues: 53.1541 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 53 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.4146 r_free = 0.4146 target = 0.131463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097612 restraints weight = 39250.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.097428 restraints weight = 26052.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097540 restraints weight = 21384.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098464 restraints weight = 16333.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.098476 restraints weight = 13695.178| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19858 Z= 0.153 Angle : 0.601 7.483 27598 Z= 0.329 Chirality : 0.040 0.148 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.373 84.315 3740 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.39 % Allowed : 17.07 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1936 helix: 1.62 (0.19), residues: 818 sheet: 0.07 (0.28), residues: 382 loop : -0.51 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 159 TYR 0.014 0.001 TYR A 77 PHE 0.012 0.001 PHE G 23 TRP 0.023 0.001 TRP E 208 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (19826) covalent geometry : angle 0.59905 / 0.33 (27584) hydrogen bonds : bond 0.03488 / 2.42 ( 960) hydrogen bonds : angle 4.91088 / 3.53 ( 2588) metal coordination : bond 0.00662 / 0.46 ( 32) metal coordination : angle 2.14494 / 1.14 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.24 seconds wall clock time: 51 minutes 58.09 seconds (3118.09 seconds total)