Starting phenix.real_space_refine on Thu Mar 5 03:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usf_26737/03_2026/7usf_26737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usf_26737/03_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_26737/03_2026/7usf_26737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usf_26737/03_2026/7usf_26737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/03_2026/7usf_26737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usf_26737/03_2026/7usf_26737.map" } 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-5986/lib/python3.9/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: 4.15, per 1000 atoms: 0.22 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: 1.53 Conformation dependent library (CDL) restraints added in 623.4 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: 2.33 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: 3.55 Time building geometry restraints manager: 2.11 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=" C THR E 121 " pdb=" N ASP E 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C THR A 121 " pdb=" N ASP A 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C ILE B 147 " pdb=" N PRO B 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" C ILE F 147 " pdb=" N PRO F 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" CB ASN C 123 " pdb=" CG ASN C 123 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 19821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27170 2.05 - 4.10: 392 4.10 - 6.15: 18 6.15 - 8.20: 2 8.20 - 10.25: 2 Bond angle restraints: 27584 Sorted by residual: angle pdb=" N THR C 226 " pdb=" CA THR C 226 " pdb=" C THR C 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N THR G 226 " pdb=" CA THR G 226 " pdb=" C THR G 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N VAL H 194 " pdb=" CA VAL H 194 " pdb=" C VAL H 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N VAL D 194 " pdb=" CA VAL D 194 " pdb=" C VAL D 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N GLY F 209 " pdb=" CA GLY F 209 " pdb=" C GLY F 209 " ideal model delta sigma weight residual 112.34 118.68 -6.34 2.04e+00 2.40e-01 9.66e+00 ... (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: 2162 0.036 - 0.071: 622 0.071 - 0.107: 176 0.107 - 0.143: 36 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: 0.03 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: 1.440 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.770 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.003 0.040 19858 Z= 0.143 Angle : 0.600 20.278 27598 Z= 0.322 Chirality : 0.038 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 covalent geometry : bond 0.00291 (19826) covalent geometry : angle 0.55285 (27584) hydrogen bonds : bond 0.13779 ( 960) hydrogen bonds : angle 6.48990 ( 2588) metal coordination : bond 0.01488 ( 32) metal coordination : angle 10.38485 ( 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 : 0.657 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: 0.6938 (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: 0.6936 (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: 0.1324 time to fit residues: 64.5713 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 : 0.545 ------------------------------------------------------------------------------- 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: 3.9990 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 68 HIS C 192 ASN C 201 HIS ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096319 restraints weight = 39525.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096359 restraints weight = 25980.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096458 restraints weight = 19715.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096937 restraints weight = 15754.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.097116 restraints weight = 14334.037| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19858 Z= 0.216 Angle : 0.588 6.493 27598 Z= 0.324 Chirality : 0.041 0.133 3002 Planarity : 0.004 0.041 3000 Dihedral : 21.929 84.857 3740 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.27 % Allowed : 8.75 % Favored : 89.99 % 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: 0.77 (0.20), residues: 1936 helix: 1.42 (0.18), residues: 818 sheet: 0.52 (0.29), residues: 362 loop : -0.41 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 20 TYR 0.017 0.002 TYR C 77 PHE 0.018 0.002 PHE C 23 TRP 0.018 0.001 TRP B 208 HIS 0.008 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00494 (19826) covalent geometry : angle 0.58578 (27584) hydrogen bonds : bond 0.03991 ( 960) hydrogen bonds : angle 5.24382 ( 2588) metal coordination : bond 0.00890 ( 32) metal coordination : angle 2.36625 ( 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 267 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.501 Fit side-chains REVERT: B 3 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 130 ARG cc_start: 0.7723 (mmp-170) cc_final: 0.7508 (mmp80) REVERT: B 201 HIS cc_start: 0.7536 (m-70) cc_final: 0.7244 (m-70) REVERT: C 65 ASP cc_start: 0.8635 (t70) cc_final: 0.8353 (t0) REVERT: C 205 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8532 (mt-10) REVERT: D 20 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.8177 (ptm-80) REVERT: D 59 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7380 (mpp80) REVERT: D 134 GLU cc_start: 0.8361 (mp0) cc_final: 0.7670 (mp0) REVERT: D 161 HIS cc_start: 0.7347 (m-70) cc_final: 0.6752 (m90) REVERT: D 195 ASN cc_start: 0.8669 (m-40) cc_final: 0.8264 (t0) REVERT: D 196 MET cc_start: 0.7183 (mmm) cc_final: 0.6579 (mmm) REVERT: D 205 GLU cc_start: 0.8332 (mp0) cc_final: 0.7426 (mp0) REVERT: D 223 ASP cc_start: 0.8289 (t70) cc_final: 0.8022 (t0) REVERT: D 251 GLU cc_start: 0.7748 (tp30) cc_final: 0.7467 (tp30) REVERT: D 265 THR cc_start: 0.8107 (m) cc_final: 0.7761 (p) REVERT: D 269 GLU cc_start: 0.5926 (pt0) cc_final: 0.5583 (pt0) REVERT: F 3 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6976 (mm-30) REVERT: F 130 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.7507 (mmp80) REVERT: F 201 HIS cc_start: 0.7532 (m-70) cc_final: 0.7240 (m-70) REVERT: G 65 ASP cc_start: 0.8635 (t70) cc_final: 0.8355 (t0) REVERT: G 205 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8531 (mt-10) REVERT: H 20 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.8173 (ptm-80) REVERT: H 59 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7383 (mpp80) REVERT: H 134 GLU cc_start: 0.8347 (mp0) cc_final: 0.7662 (mp0) REVERT: H 161 HIS cc_start: 0.7348 (m-70) cc_final: 0.6745 (m90) REVERT: H 195 ASN cc_start: 0.8668 (m-40) cc_final: 0.8263 (t0) REVERT: H 196 MET cc_start: 0.7182 (mmm) cc_final: 0.6578 (mmm) REVERT: H 205 GLU cc_start: 0.8333 (mp0) cc_final: 0.7429 (mp0) REVERT: H 223 ASP cc_start: 0.8286 (t70) cc_final: 0.8020 (t0) REVERT: H 251 GLU cc_start: 0.7745 (tp30) cc_final: 0.7464 (tp30) REVERT: H 265 THR cc_start: 0.8103 (m) cc_final: 0.7758 (p) REVERT: H 269 GLU cc_start: 0.5926 (pt0) cc_final: 0.5586 (pt0) outliers start: 21 outliers final: 15 residues processed: 257 average time/residue: 0.1370 time to fit residues: 54.0794 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 119 ILE 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 F residue 132 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 119 ILE 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: 2.9990 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN C 161 HIS ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN E 52 ASN G 161 HIS G 201 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.128162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093252 restraints weight = 39573.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091342 restraints weight = 24711.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092195 restraints weight = 19250.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092469 restraints weight = 15146.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092596 restraints weight = 14031.915| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19858 Z= 0.166 Angle : 0.549 6.458 27598 Z= 0.299 Chirality : 0.039 0.136 3002 Planarity : 0.004 0.039 3000 Dihedral : 21.846 84.567 3740 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.81 % Allowed : 10.74 % Favored : 87.45 % 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: 0.84 (0.20), residues: 1936 helix: 1.54 (0.18), residues: 820 sheet: 0.61 (0.29), residues: 362 loop : -0.51 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 94 TYR 0.015 0.001 TYR C 77 PHE 0.013 0.001 PHE G 23 TRP 0.015 0.001 TRP B 208 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00375 (19826) covalent geometry : angle 0.54671 (27584) hydrogen bonds : bond 0.03586 ( 960) hydrogen bonds : angle 5.06322 ( 2588) metal coordination : bond 0.00695 ( 32) metal coordination : angle 2.40834 ( 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 254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 ASP cc_start: 0.8671 (t70) cc_final: 0.8395 (t0) REVERT: C 169 ASN cc_start: 0.6846 (m-40) cc_final: 0.5902 (t0) REVERT: C 205 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8547 (mt-10) REVERT: D 59 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7263 (mpp80) REVERT: D 134 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: D 159 ARG cc_start: 0.8836 (tpt90) cc_final: 0.8497 (tpt90) REVERT: D 196 MET cc_start: 0.7256 (mmm) cc_final: 0.6425 (mmm) REVERT: D 205 GLU cc_start: 0.8286 (mp0) cc_final: 0.7518 (mp0) REVERT: D 269 GLU cc_start: 0.5997 (pt0) cc_final: 0.5657 (pt0) REVERT: G 65 ASP cc_start: 0.8679 (t70) cc_final: 0.8398 (t0) REVERT: G 169 ASN cc_start: 0.6850 (m-40) cc_final: 0.5901 (t0) REVERT: G 205 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8551 (mt-10) REVERT: H 59 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7257 (mpp80) REVERT: H 134 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: H 159 ARG cc_start: 0.8854 (tpt90) cc_final: 0.8512 (tpt90) REVERT: H 196 MET cc_start: 0.7265 (mmm) cc_final: 0.6427 (mmm) REVERT: H 205 GLU cc_start: 0.8294 (mp0) cc_final: 0.7520 (mp0) REVERT: H 269 GLU cc_start: 0.5997 (pt0) cc_final: 0.5656 (pt0) outliers start: 30 outliers final: 13 residues processed: 244 average time/residue: 0.1326 time to fit residues: 50.0627 Evaluate side-chains 215 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 34 VAL 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 131 SER Chi-restraints excluded: chain H residue 134 GLU 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: 6.9990 chunk 147 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 171 optimal weight: 0.0070 chunk 205 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN C 29 GLN D 162 GLN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN ** H 182 HIS ** 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 = 0.4083 r_free = 0.4083 target = 0.130706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094162 restraints weight = 39434.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092980 restraints weight = 21389.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093603 restraints weight = 17110.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093997 restraints weight = 13444.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094129 restraints weight = 12448.843| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19858 Z= 0.135 Angle : 0.532 8.880 27598 Z= 0.290 Chirality : 0.038 0.132 3002 Planarity : 0.004 0.034 3000 Dihedral : 21.781 82.688 3740 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.29 % Allowed : 12.00 % Favored : 85.71 % 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: 0.93 (0.20), residues: 1936 helix: 1.67 (0.18), residues: 822 sheet: 0.54 (0.29), residues: 368 loop : -0.48 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 20 TYR 0.011 0.001 TYR A 77 PHE 0.011 0.001 PHE C 23 TRP 0.015 0.001 TRP B 208 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00302 (19826) covalent geometry : angle 0.52876 (27584) hydrogen bonds : bond 0.03268 ( 960) hydrogen bonds : angle 4.92345 ( 2588) metal coordination : bond 0.00652 ( 32) metal coordination : angle 2.46052 ( 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 261 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 220 MET cc_start: 0.7910 (mmm) cc_final: 0.7650 (mmm) REVERT: C 62 TRP cc_start: 0.7223 (m-10) cc_final: 0.6789 (m-10) REVERT: C 65 ASP cc_start: 0.8762 (t0) cc_final: 0.8449 (t0) REVERT: C 169 ASN cc_start: 0.6903 (m-40) cc_final: 0.6003 (t0) REVERT: C 205 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8535 (mt-10) REVERT: D 15 ASN cc_start: 0.7978 (m-40) cc_final: 0.7432 (p0) REVERT: D 59 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7226 (mpp80) REVERT: D 62 TRP cc_start: 0.7126 (m-10) cc_final: 0.6842 (m-10) REVERT: D 134 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: D 196 MET cc_start: 0.7471 (mmm) cc_final: 0.7100 (mmm) REVERT: D 202 THR cc_start: 0.6059 (OUTLIER) cc_final: 0.5615 (p) REVERT: D 205 GLU cc_start: 0.8339 (mp0) cc_final: 0.7640 (mp0) REVERT: D 251 GLU cc_start: 0.7851 (tp30) cc_final: 0.7548 (tp30) REVERT: D 269 GLU cc_start: 0.6061 (pt0) cc_final: 0.5717 (pt0) REVERT: F 3 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6863 (mm-30) REVERT: F 220 MET cc_start: 0.7903 (mmm) cc_final: 0.7647 (mmm) REVERT: G 62 TRP cc_start: 0.7238 (m-10) cc_final: 0.6805 (m-10) REVERT: G 65 ASP cc_start: 0.8760 (t0) cc_final: 0.8447 (t0) REVERT: G 169 ASN cc_start: 0.6893 (m-40) cc_final: 0.5994 (t0) REVERT: G 205 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8531 (mt-10) REVERT: H 15 ASN cc_start: 0.7979 (m-40) cc_final: 0.7437 (p0) REVERT: H 59 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7222 (mpp80) REVERT: H 62 TRP cc_start: 0.7136 (m-10) cc_final: 0.6850 (m-10) REVERT: H 134 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: H 196 MET cc_start: 0.7477 (mmm) cc_final: 0.7094 (mmm) REVERT: H 202 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5620 (p) REVERT: H 205 GLU cc_start: 0.8347 (mp0) cc_final: 0.7640 (mp0) REVERT: H 251 GLU cc_start: 0.7860 (tp30) cc_final: 0.7556 (tp30) REVERT: H 269 GLU cc_start: 0.6067 (pt0) cc_final: 0.5718 (pt0) outliers start: 38 outliers final: 12 residues processed: 249 average time/residue: 0.1311 time to fit residues: 50.5422 Evaluate side-chains 222 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL 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 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.129452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094084 restraints weight = 39311.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092098 restraints weight = 24698.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092980 restraints weight = 19642.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093230 restraints weight = 15327.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093367 restraints weight = 14297.400| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19858 Z= 0.160 Angle : 0.547 8.858 27598 Z= 0.298 Chirality : 0.039 0.133 3002 Planarity : 0.004 0.034 3000 Dihedral : 21.897 83.912 3740 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.69 % Allowed : 13.81 % Favored : 84.50 % 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: 0.91 (0.20), residues: 1936 helix: 1.70 (0.19), residues: 822 sheet: 0.42 (0.29), residues: 380 loop : -0.51 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 27 TYR 0.013 0.001 TYR E 77 PHE 0.012 0.001 PHE C 23 TRP 0.016 0.001 TRP F 208 HIS 0.007 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00361 (19826) covalent geometry : angle 0.54486 (27584) hydrogen bonds : bond 0.03376 ( 960) hydrogen bonds : angle 4.88405 ( 2588) metal coordination : bond 0.00709 ( 32) metal coordination : angle 2.08861 ( 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 248 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7755 (mmm) cc_final: 0.7486 (mmm) REVERT: C 65 ASP cc_start: 0.8702 (t0) cc_final: 0.8456 (t0) REVERT: C 85 TYR cc_start: 0.7190 (t80) cc_final: 0.6649 (t80) REVERT: C 169 ASN cc_start: 0.6498 (m-40) cc_final: 0.5955 (t0) REVERT: C 205 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8506 (mt-10) REVERT: D 15 ASN cc_start: 0.7948 (m-40) cc_final: 0.7529 (p0) REVERT: D 59 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7946 (mpp80) REVERT: D 134 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: D 196 MET cc_start: 0.7120 (mmm) cc_final: 0.6344 (mmm) REVERT: D 205 GLU cc_start: 0.8325 (mp0) cc_final: 0.7816 (mp0) REVERT: D 251 GLU cc_start: 0.7747 (tp30) cc_final: 0.7470 (tp30) REVERT: D 269 GLU cc_start: 0.6030 (pt0) cc_final: 0.5694 (pt0) REVERT: F 220 MET cc_start: 0.7736 (mmm) cc_final: 0.7485 (mmm) REVERT: G 65 ASP cc_start: 0.8712 (t0) cc_final: 0.8457 (t0) REVERT: G 85 TYR cc_start: 0.7189 (t80) cc_final: 0.6643 (t80) REVERT: G 169 ASN cc_start: 0.6499 (m-40) cc_final: 0.5955 (t0) REVERT: G 205 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8507 (mt-10) REVERT: H 15 ASN cc_start: 0.7945 (m-40) cc_final: 0.7521 (p0) REVERT: H 59 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7946 (mpp80) REVERT: H 134 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: H 196 MET cc_start: 0.7123 (mmm) cc_final: 0.6346 (mmm) REVERT: H 205 GLU cc_start: 0.8326 (mp0) cc_final: 0.7820 (mp0) REVERT: H 251 GLU cc_start: 0.7755 (tp30) cc_final: 0.7479 (tp30) REVERT: H 269 GLU cc_start: 0.6030 (pt0) cc_final: 0.5696 (pt0) outliers start: 28 outliers final: 15 residues processed: 242 average time/residue: 0.1368 time to fit residues: 50.9861 Evaluate side-chains 215 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN 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 E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 131 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 0.1980 chunk 195 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** 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 = 0.4092 r_free = 0.4092 target = 0.131178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093241 restraints weight = 39044.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093937 restraints weight = 20944.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094882 restraints weight = 13478.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094911 restraints weight = 11371.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095015 restraints weight = 10749.570| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19858 Z= 0.127 Angle : 0.536 7.075 27598 Z= 0.292 Chirality : 0.038 0.129 3002 Planarity : 0.004 0.035 3000 Dihedral : 21.764 81.372 3740 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 15.62 % Favored : 82.87 % 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: 1.01 (0.20), residues: 1936 helix: 1.79 (0.19), residues: 820 sheet: 0.37 (0.28), residues: 396 loop : -0.40 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 159 TYR 0.009 0.001 TYR D 242 PHE 0.024 0.001 PHE C 21 TRP 0.019 0.001 TRP A 208 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00284 (19826) covalent geometry : angle 0.53364 (27584) hydrogen bonds : bond 0.03030 ( 960) hydrogen bonds : angle 4.78254 ( 2588) metal coordination : bond 0.00684 ( 32) metal coordination : angle 2.16608 ( 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 249 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7931 (mmm) cc_final: 0.7571 (mmm) REVERT: C 64 MET cc_start: 0.7660 (ttp) cc_final: 0.7438 (ttm) REVERT: C 65 ASP cc_start: 0.8764 (t0) cc_final: 0.8442 (t0) REVERT: C 85 TYR cc_start: 0.7398 (t80) cc_final: 0.6840 (t80) REVERT: C 169 ASN cc_start: 0.6572 (m-40) cc_final: 0.5909 (t0) REVERT: C 205 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 15 ASN cc_start: 0.7848 (m-40) cc_final: 0.7176 (p0) REVERT: D 134 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: D 195 ASN cc_start: 0.8681 (t0) cc_final: 0.7340 (m110) REVERT: D 196 MET cc_start: 0.7263 (mmm) cc_final: 0.6887 (mmt) REVERT: D 205 GLU cc_start: 0.8441 (mp0) cc_final: 0.7620 (mp0) REVERT: D 251 GLU cc_start: 0.7646 (tp30) cc_final: 0.7282 (tp30) REVERT: D 269 GLU cc_start: 0.6024 (pt0) cc_final: 0.5707 (pt0) REVERT: F 220 MET cc_start: 0.7926 (mmm) cc_final: 0.7594 (mmm) REVERT: G 64 MET cc_start: 0.7658 (ttp) cc_final: 0.7434 (ttm) REVERT: G 65 ASP cc_start: 0.8764 (t0) cc_final: 0.8443 (t0) REVERT: G 85 TYR cc_start: 0.7401 (t80) cc_final: 0.6842 (t80) REVERT: G 169 ASN cc_start: 0.6567 (m-40) cc_final: 0.5906 (t0) REVERT: G 205 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8605 (mt-10) REVERT: H 15 ASN cc_start: 0.7843 (m-40) cc_final: 0.7172 (p0) REVERT: H 134 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: H 195 ASN cc_start: 0.8676 (t0) cc_final: 0.7334 (m110) REVERT: H 196 MET cc_start: 0.7268 (mmm) cc_final: 0.6883 (mmt) REVERT: H 205 GLU cc_start: 0.8447 (mp0) cc_final: 0.7629 (mp0) REVERT: H 251 GLU cc_start: 0.7652 (tp30) cc_final: 0.7282 (tp30) REVERT: H 269 GLU cc_start: 0.6022 (pt0) cc_final: 0.5705 (pt0) outliers start: 25 outliers final: 18 residues processed: 243 average time/residue: 0.1406 time to fit residues: 53.0951 Evaluate side-chains 217 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN 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 D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN 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 Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 16 optimal weight: 0.9980 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.129523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093599 restraints weight = 39418.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091979 restraints weight = 24963.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092831 restraints weight = 20428.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093111 restraints weight = 16814.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093206 restraints weight = 14688.036| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19858 Z= 0.160 Angle : 0.557 8.307 27598 Z= 0.303 Chirality : 0.039 0.136 3002 Planarity : 0.004 0.035 3000 Dihedral : 21.932 83.136 3740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.33 % Allowed : 16.77 % Favored : 81.91 % 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: 0.97 (0.20), residues: 1936 helix: 1.78 (0.19), residues: 822 sheet: 0.35 (0.28), residues: 396 loop : -0.47 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 159 TYR 0.012 0.001 TYR A 77 PHE 0.015 0.001 PHE C 21 TRP 0.022 0.001 TRP A 208 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00361 (19826) covalent geometry : angle 0.55535 (27584) hydrogen bonds : bond 0.03256 ( 960) hydrogen bonds : angle 4.81444 ( 2588) metal coordination : bond 0.00707 ( 32) metal coordination : angle 2.02614 ( 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 230 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7818 (mmm) cc_final: 0.7566 (mmm) REVERT: C 65 ASP cc_start: 0.8733 (t0) cc_final: 0.8438 (t0) REVERT: C 85 TYR cc_start: 0.7549 (t80) cc_final: 0.7077 (t80) REVERT: C 158 GLU cc_start: 0.7627 (tp30) cc_final: 0.7219 (tp30) REVERT: C 169 ASN cc_start: 0.6404 (m-40) cc_final: 0.5868 (t0) REVERT: C 205 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8519 (mt-10) REVERT: D 15 ASN cc_start: 0.7864 (m-40) cc_final: 0.7228 (p0) REVERT: D 134 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: D 195 ASN cc_start: 0.8622 (t0) cc_final: 0.7469 (m110) REVERT: D 196 MET cc_start: 0.7107 (mmm) cc_final: 0.6774 (mmt) REVERT: D 205 GLU cc_start: 0.8541 (mp0) cc_final: 0.7742 (mp0) REVERT: D 251 GLU cc_start: 0.7696 (tp30) cc_final: 0.7419 (tp30) REVERT: D 269 GLU cc_start: 0.6025 (pt0) cc_final: 0.5692 (pt0) REVERT: F 220 MET cc_start: 0.7812 (mmm) cc_final: 0.7571 (mmm) REVERT: G 65 ASP cc_start: 0.8729 (t0) cc_final: 0.8432 (t0) REVERT: G 85 TYR cc_start: 0.7543 (t80) cc_final: 0.7068 (t80) REVERT: G 158 GLU cc_start: 0.7624 (tp30) cc_final: 0.7214 (tp30) REVERT: G 169 ASN cc_start: 0.6402 (m-40) cc_final: 0.5867 (t0) REVERT: G 205 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8514 (mt-10) REVERT: H 15 ASN cc_start: 0.7857 (m-40) cc_final: 0.7226 (p0) REVERT: H 134 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: H 195 ASN cc_start: 0.8620 (t0) cc_final: 0.7466 (m110) REVERT: H 196 MET cc_start: 0.7101 (mmm) cc_final: 0.6756 (mmt) REVERT: H 205 GLU cc_start: 0.8548 (mp0) cc_final: 0.7748 (mp0) REVERT: H 251 GLU cc_start: 0.7699 (tp30) cc_final: 0.7423 (tp30) REVERT: H 269 GLU cc_start: 0.6032 (pt0) cc_final: 0.5697 (pt0) outliers start: 22 outliers final: 19 residues processed: 226 average time/residue: 0.1358 time to fit residues: 47.2309 Evaluate side-chains 225 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 234 VAL 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 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 34 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 26 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 153 optimal weight: 0.3980 chunk 181 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN C 63 GLN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091727 restraints weight = 39347.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.090080 restraints weight = 24847.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090847 restraints weight = 20533.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.091134 restraints weight = 16704.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.091222 restraints weight = 14586.615| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19858 Z= 0.199 Angle : 0.587 9.241 27598 Z= 0.320 Chirality : 0.040 0.154 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.146 86.993 3740 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.87 % Allowed : 17.01 % Favored : 81.12 % 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: 0.88 (0.20), residues: 1936 helix: 1.70 (0.19), residues: 818 sheet: 0.50 (0.29), residues: 364 loop : -0.58 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 20 TYR 0.015 0.001 TYR A 77 PHE 0.013 0.001 PHE C 21 TRP 0.024 0.001 TRP A 208 HIS 0.008 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00454 (19826) covalent geometry : angle 0.58590 (27584) hydrogen bonds : bond 0.03543 ( 960) hydrogen bonds : angle 4.89989 ( 2588) metal coordination : bond 0.00931 ( 32) metal coordination : angle 1.99053 ( 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 230 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7872 (mmm) cc_final: 0.7639 (mmm) REVERT: C 65 ASP cc_start: 0.8565 (t0) cc_final: 0.8310 (t0) REVERT: C 85 TYR cc_start: 0.7526 (t80) cc_final: 0.7207 (t80) REVERT: C 158 GLU cc_start: 0.7660 (tp30) cc_final: 0.7255 (tp30) REVERT: C 169 ASN cc_start: 0.6429 (m-40) cc_final: 0.5894 (t0) REVERT: C 205 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8561 (mt-10) REVERT: D 15 ASN cc_start: 0.7923 (m-40) cc_final: 0.7299 (p0) REVERT: D 134 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: D 195 ASN cc_start: 0.8604 (t0) cc_final: 0.7236 (m110) REVERT: D 205 GLU cc_start: 0.8543 (mp0) cc_final: 0.7735 (mp0) REVERT: D 251 GLU cc_start: 0.7675 (tp30) cc_final: 0.7385 (tp30) REVERT: D 269 GLU cc_start: 0.6125 (pt0) cc_final: 0.5797 (pt0) REVERT: F 220 MET cc_start: 0.7863 (mmm) cc_final: 0.7641 (mmm) REVERT: G 65 ASP cc_start: 0.8561 (t0) cc_final: 0.8304 (t0) REVERT: G 85 TYR cc_start: 0.7521 (t80) cc_final: 0.7203 (t80) REVERT: G 158 GLU cc_start: 0.7655 (tp30) cc_final: 0.7253 (tp30) REVERT: G 169 ASN cc_start: 0.6421 (m-40) cc_final: 0.5887 (t0) REVERT: G 205 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8556 (mt-10) REVERT: H 15 ASN cc_start: 0.7916 (m-40) cc_final: 0.7300 (p0) REVERT: H 134 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: H 195 ASN cc_start: 0.8597 (t0) cc_final: 0.7225 (m110) REVERT: H 205 GLU cc_start: 0.8546 (mp0) cc_final: 0.7742 (mp0) REVERT: H 251 GLU cc_start: 0.7683 (tp30) cc_final: 0.7390 (tp30) REVERT: H 269 GLU cc_start: 0.6130 (pt0) cc_final: 0.5796 (pt0) outliers start: 31 outliers final: 25 residues processed: 220 average time/residue: 0.1317 time to fit residues: 45.0741 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 113 MET 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 34 VAL 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 G residue 26 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 113 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.128912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092949 restraints weight = 39220.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092480 restraints weight = 21515.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093137 restraints weight = 16377.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093646 restraints weight = 13497.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.093607 restraints weight = 11987.124| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19858 Z= 0.134 Angle : 0.562 9.986 27598 Z= 0.304 Chirality : 0.038 0.133 3002 Planarity : 0.004 0.036 3000 Dihedral : 21.898 82.357 3740 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.21 % Allowed : 17.91 % Favored : 80.88 % 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: 0.99 (0.20), residues: 1936 helix: 1.79 (0.19), residues: 820 sheet: 0.37 (0.28), residues: 396 loop : -0.45 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 20 TYR 0.010 0.001 TYR F 177 PHE 0.015 0.001 PHE C 21 TRP 0.025 0.001 TRP A 208 HIS 0.006 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00301 (19826) covalent geometry : angle 0.55994 (27584) hydrogen bonds : bond 0.03075 ( 960) hydrogen bonds : angle 4.76373 ( 2588) metal coordination : bond 0.00808 ( 32) metal coordination : angle 2.35622 ( 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 222 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7913 (mmm) cc_final: 0.7623 (mmm) REVERT: C 65 ASP cc_start: 0.8575 (t0) cc_final: 0.8267 (t0) REVERT: C 85 TYR cc_start: 0.7551 (t80) cc_final: 0.7292 (t80) REVERT: C 158 GLU cc_start: 0.7764 (tp30) cc_final: 0.7350 (tp30) REVERT: C 169 ASN cc_start: 0.6424 (m-40) cc_final: 0.5858 (t0) REVERT: C 205 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8602 (mt-10) REVERT: D 15 ASN cc_start: 0.7847 (m-40) cc_final: 0.7301 (p0) REVERT: D 134 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: D 195 ASN cc_start: 0.8606 (t0) cc_final: 0.7408 (m110) REVERT: D 205 GLU cc_start: 0.8462 (mp0) cc_final: 0.7610 (mp0) REVERT: D 220 MET cc_start: 0.8872 (mmm) cc_final: 0.8653 (mmm) REVERT: D 251 GLU cc_start: 0.7730 (tp30) cc_final: 0.7292 (tp30) REVERT: D 269 GLU cc_start: 0.6131 (pt0) cc_final: 0.5810 (pt0) REVERT: F 220 MET cc_start: 0.7911 (mmm) cc_final: 0.7632 (mmm) REVERT: G 65 ASP cc_start: 0.8576 (t0) cc_final: 0.8265 (t0) REVERT: G 85 TYR cc_start: 0.7513 (t80) cc_final: 0.7253 (t80) REVERT: G 113 MET cc_start: 0.6355 (mtm) cc_final: 0.6046 (mtp) REVERT: G 158 GLU cc_start: 0.7761 (tp30) cc_final: 0.7348 (tp30) REVERT: G 169 ASN cc_start: 0.6335 (m-40) cc_final: 0.5755 (t0) REVERT: G 205 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8609 (mt-10) REVERT: H 15 ASN cc_start: 0.7842 (m-40) cc_final: 0.7301 (p0) REVERT: H 134 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: H 195 ASN cc_start: 0.8596 (t0) cc_final: 0.7402 (m110) REVERT: H 205 GLU cc_start: 0.8475 (mp0) cc_final: 0.7616 (mp0) REVERT: H 220 MET cc_start: 0.8862 (mmm) cc_final: 0.8646 (mmm) REVERT: H 251 GLU cc_start: 0.7734 (tp30) cc_final: 0.7291 (tp30) REVERT: H 269 GLU cc_start: 0.6136 (pt0) cc_final: 0.5813 (pt0) outliers start: 20 outliers final: 17 residues processed: 217 average time/residue: 0.1356 time to fit residues: 46.1405 Evaluate side-chains 212 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 234 VAL 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 D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 26 THR 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 Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.091998 restraints weight = 39419.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090288 restraints weight = 24460.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091284 restraints weight = 20021.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091461 restraints weight = 16009.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091553 restraints weight = 14109.399| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19858 Z= 0.184 Angle : 0.597 9.845 27598 Z= 0.323 Chirality : 0.040 0.138 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.098 85.476 3740 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.21 % Allowed : 18.28 % Favored : 80.52 % 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: 0.91 (0.20), residues: 1936 helix: 1.68 (0.19), residues: 820 sheet: 0.45 (0.29), residues: 380 loop : -0.49 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.015 0.001 TYR E 77 PHE 0.015 0.001 PHE C 88 TRP 0.025 0.001 TRP A 208 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00421 (19826) covalent geometry : angle 0.59556 (27584) hydrogen bonds : bond 0.03424 ( 960) hydrogen bonds : angle 4.80392 ( 2588) metal coordination : bond 0.00815 ( 32) metal coordination : angle 1.96587 ( 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 215 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.7827 (mmm) cc_final: 0.7606 (mmm) REVERT: C 65 ASP cc_start: 0.8488 (t0) cc_final: 0.8240 (t0) REVERT: C 158 GLU cc_start: 0.7619 (tp30) cc_final: 0.7201 (tp30) REVERT: C 169 ASN cc_start: 0.6356 (m-40) cc_final: 0.5855 (t0) REVERT: C 205 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8529 (mt-10) REVERT: D 15 ASN cc_start: 0.7890 (m-40) cc_final: 0.7242 (p0) REVERT: D 134 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: D 143 HIS cc_start: 0.8544 (t70) cc_final: 0.8198 (t-90) REVERT: D 195 ASN cc_start: 0.8532 (t0) cc_final: 0.7614 (m110) REVERT: D 205 GLU cc_start: 0.8550 (mp0) cc_final: 0.7693 (mp0) REVERT: D 251 GLU cc_start: 0.7647 (tp30) cc_final: 0.7318 (tp30) REVERT: D 269 GLU cc_start: 0.6150 (pt0) cc_final: 0.5819 (pt0) REVERT: F 220 MET cc_start: 0.7828 (mmm) cc_final: 0.7612 (mmm) REVERT: G 65 ASP cc_start: 0.8492 (t0) cc_final: 0.8235 (t0) REVERT: G 113 MET cc_start: 0.6456 (mtm) cc_final: 0.6223 (mtp) REVERT: G 158 GLU cc_start: 0.7624 (tp30) cc_final: 0.7208 (tp30) REVERT: G 169 ASN cc_start: 0.6357 (m-40) cc_final: 0.5856 (t0) REVERT: G 205 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8552 (mt-10) REVERT: H 15 ASN cc_start: 0.7891 (m-40) cc_final: 0.7247 (p0) REVERT: H 134 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: H 143 HIS cc_start: 0.8576 (t70) cc_final: 0.8134 (t-90) REVERT: H 195 ASN cc_start: 0.8533 (t0) cc_final: 0.7615 (m110) REVERT: H 205 GLU cc_start: 0.8554 (mp0) cc_final: 0.7703 (mp0) REVERT: H 251 GLU cc_start: 0.7643 (tp30) cc_final: 0.7314 (tp30) REVERT: H 269 GLU cc_start: 0.6154 (pt0) cc_final: 0.5822 (pt0) outliers start: 20 outliers final: 18 residues processed: 211 average time/residue: 0.1344 time to fit residues: 44.0827 Evaluate side-chains 207 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL 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 D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain H residue 4 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 Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 53 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 139 optimal weight: 0.0040 chunk 184 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096713 restraints weight = 39462.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095393 restraints weight = 19523.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096690 restraints weight = 14773.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096837 restraints weight = 11835.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096887 restraints weight = 11140.450| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19858 Z= 0.128 Angle : 0.573 10.640 27598 Z= 0.308 Chirality : 0.038 0.130 3002 Planarity : 0.004 0.038 3000 Dihedral : 21.812 80.661 3740 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.21 % Allowed : 18.70 % Favored : 80.10 % 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: 0.93 (0.20), residues: 1936 helix: 1.77 (0.19), residues: 820 sheet: 0.24 (0.28), residues: 386 loop : -0.44 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 130 TYR 0.015 0.001 TYR G 112 PHE 0.016 0.001 PHE G 21 TRP 0.025 0.001 TRP A 208 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00290 (19826) covalent geometry : angle 0.57054 (27584) hydrogen bonds : bond 0.02987 ( 960) hydrogen bonds : angle 4.70354 ( 2588) metal coordination : bond 0.00844 ( 32) metal coordination : angle 2.23445 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.49 seconds wall clock time: 48 minutes 37.42 seconds (2917.42 seconds total)