Starting phenix.real_space_refine on Sat Sep 12 22:28:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usf_26737/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.map" model { file = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usf_26737/09_2026/7usf_26737.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 8 6.06 5 P 150 5.49 5 S 64 5.16 5 C 11632 2.51 5 N 3472 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2121 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain: "B" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2019 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Chain: "C" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1922 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1871 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 79.129 110.276 55.058 1.00101.43 S ATOM 320 SG CYS A 40 78.963 106.675 56.185 1.00103.87 S ATOM 2420 SG CYS B 37 14.537 81.224 45.444 1.00121.13 S ATOM 2441 SG CYS B 40 14.038 77.220 46.958 1.00123.63 S ATOM 4435 SG CYS C 37 40.874 151.914 71.798 1.00204.27 S ATOM 4456 SG CYS C 40 38.126 149.786 70.059 1.00204.91 S ATOM 6325 SG CYS D 37 50.304 127.400 26.565 1.00181.93 S ATOM 6346 SG CYS D 40 52.486 127.361 29.823 1.00187.21 S Restraints were copied for chains: E, F, G, H, L, M, N Time building chain proxies: 5.43, per 1000 atoms: 0.29 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: 1.79 Conformation dependent library (CDL) restraints added in 709.0 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: 2.34 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: 3.88 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5270 1.34 - 1.45: 4410 1.45 - 1.57: 9746 1.57 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19826 Sorted by residual: bond pdb=" C3' DA M 20 " pdb=" C2' DA M 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA J 20 " pdb=" C2' DA J 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG N 10 " pdb=" C2' DG N 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DG K 10 " pdb=" C2' DG K 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DC M 27 " pdb=" C2' DC M 27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 ... (remaining 19821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27028 2.05 - 4.10: 536 4.10 - 6.15: 16 6.15 - 8.20: 2 8.20 - 10.25: 2 Bond angle restraints: 27584 Sorted by residual: angle pdb=" N3 DT M 31 " pdb=" C4 DT M 31 " pdb=" O4 DT M 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 32 " pdb=" C4 DT J 32 " pdb=" O4 DT J 32 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT M 32 " pdb=" C4 DT M 32 " pdb=" O4 DT M 32 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9380 17.97 - 35.93: 1096 35.93 - 53.90: 586 53.90 - 71.87: 160 71.87 - 89.83: 12 Dihedral angle restraints: 11234 sinusoidal: 5438 harmonic: 5796 Sorted by residual: dihedral pdb=" CA TRP H 139 " pdb=" C TRP H 139 " pdb=" N LYS H 140 " pdb=" CA LYS H 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP D 139 " pdb=" C TRP D 139 " pdb=" N LYS D 140 " pdb=" CA LYS D 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY B 209 " pdb=" C GLY B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 11231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1948 0.036 - 0.071: 748 0.071 - 0.107: 256 0.107 - 0.143: 44 0.143 - 0.178: 6 Chirality restraints: 3002 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA TRP D 139 " pdb=" N TRP D 139 " pdb=" C TRP D 139 " pdb=" CB TRP D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2999 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN G 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN G 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA G 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN C 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN C 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 139 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.29e+00 pdb=" CG TRP D 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 139 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 139 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 126 2.59 - 3.17: 15458 3.17 - 3.75: 32720 3.75 - 4.32: 43088 4.32 - 4.90: 68437 Nonbonded interactions: 159829 Sorted by model distance: nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.017 3.040 nonbonded pdb=" OG1 THR D 202 " pdb=" OE1 GLU D 205 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASP A 65 " pdb="CA CA A 501 " model vdw 2.209 2.510 nonbonded pdb=" OD1 ASP E 65 " pdb="CA CA E 501 " model vdw 2.209 2.510 nonbonded pdb=" OH TYR C 242 " pdb=" OP1 DG L 10 " model vdw 2.219 3.040 ... (remaining 159824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19858 Z= 0.311 Angle : 0.655 20.278 27598 Z= 0.444 Chirality : 0.042 0.178 3002 Planarity : 0.004 0.052 3000 Dihedral : 19.616 89.833 7458 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1936 helix: 1.58 (0.18), residues: 810 sheet: 0.37 (0.30), residues: 342 loop : -0.47 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.015 0.001 TYR H 127 PHE 0.018 0.001 PHE G 88 TRP 0.041 0.002 TRP D 139 HIS 0.012 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.31 (19826) covalent geometry : angle 0.61176 / 0.44 (27584) hydrogen bonds : bond 0.13779 / 9.59 ( 960) hydrogen bonds : angle 6.48990 / 4.72 ( 2588) metal coordination : bond 0.01488 / 0.88 ( 32) metal coordination : angle 10.38485 / 6.03 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8452 (mmm) cc_final: 0.8179 (mmm) REVERT: A 244 CYS cc_start: 0.8664 (t) cc_final: 0.8120 (t) REVERT: B 130 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7631 (mmp80) REVERT: B 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7891 (m-70) REVERT: B 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6994 (tpt) REVERT: B 242 TYR cc_start: 0.8140 (m-10) cc_final: 0.7903 (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: 0.7061 (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: 0.6793 (mmm) REVERT: D 205 GLU cc_start: 0.8167 (mp0) cc_final: 0.7170 (mp0) REVERT: E 218 MET cc_start: 0.8460 (mmm) cc_final: 0.8186 (mmm) REVERT: E 244 CYS cc_start: 0.8671 (t) cc_final: 0.8128 (t) REVERT: F 130 ARG cc_start: 0.7952 (mmp-170) cc_final: 0.7632 (mmp80) REVERT: F 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7890 (m-70) REVERT: F 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6992 (tpt) REVERT: F 242 TYR cc_start: 0.8139 (m-10) cc_final: 0.7899 (m-10) REVERT: F 254 ILE cc_start: 0.8547 (mt) cc_final: 0.8321 (tt) REVERT: G 64 MET cc_start: 0.7824 (ttp) cc_final: 0.7598 (ttm) REVERT: G 65 ASP cc_start: 0.8301 (t0) cc_final: 0.8016 (t0) REVERT: G 85 TYR cc_start: 0.7383 (t80) cc_final: 0.7019 (t80) REVERT: G 110 PHE cc_start: 0.8496 (m-10) cc_final: 0.7891 (m-10) REVERT: G 196 MET cc_start: 0.8001 (ptp) cc_final: 0.6738 (ptp) REVERT: G 205 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8670 (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: 0.8574 (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: 0.1417 time to fit residues: 69.3359 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 192 ASN B 68 HIS C 12 HIS C 161 HIS C 192 ASN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 192 ASN F 68 HIS G 12 HIS G 161 HIS G 192 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.092390 restraints weight = 39805.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092498 restraints weight = 20787.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093132 restraints weight = 14943.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093751 restraints weight = 12722.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093802 restraints weight = 11882.213| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19858 Z= 0.206 Angle : 0.614 7.467 27598 Z= 0.340 Chirality : 0.043 0.177 3002 Planarity : 0.004 0.047 3000 Dihedral : 22.226 82.098 3740 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 8.08 % Favored : 90.95 % 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: 1.55 (0.18), residues: 828 sheet: 0.39 (0.29), residues: 350 loop : -0.49 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 27 TYR 0.020 0.001 TYR H 242 PHE 0.018 0.002 PHE C 189 TRP 0.012 0.001 TRP B 208 HIS 0.009 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (19826) covalent geometry : angle 0.61189 / 0.34 (27584) hydrogen bonds : bond 0.04485 / 3.10 ( 960) hydrogen bonds : angle 5.45131 / 3.95 ( 2588) metal coordination : bond 0.00905 / 0.61 ( 32) metal coordination : angle 2.39292 / 1.05 ( 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 268 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 252 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 ARG cc_start: 0.7810 (mmp-170) cc_final: 0.7552 (mmp80) REVERT: B 134 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 201 HIS cc_start: 0.7734 (m-70) cc_final: 0.7400 (m-70) REVERT: B 220 MET cc_start: 0.7877 (tpt) cc_final: 0.7314 (tpt) REVERT: C 62 TRP cc_start: 0.7147 (m-10) cc_final: 0.6867 (m-10) REVERT: C 65 ASP cc_start: 0.8510 (t0) cc_final: 0.8282 (t0) REVERT: C 85 TYR cc_start: 0.7394 (t80) cc_final: 0.7070 (t80) REVERT: C 127 TYR cc_start: 0.6876 (m-10) cc_final: 0.6624 (m-10) REVERT: C 141 ILE cc_start: 0.8266 (mt) cc_final: 0.7988 (tt) REVERT: C 205 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8670 (mt-10) REVERT: D 7 GLU cc_start: 0.8795 (pt0) cc_final: 0.8489 (pm20) REVERT: D 134 GLU cc_start: 0.8451 (mp0) cc_final: 0.8051 (tm-30) REVERT: D 138 ARG cc_start: 0.7323 (ttt180) cc_final: 0.7064 (tpt-90) REVERT: D 161 HIS cc_start: 0.7363 (m-70) cc_final: 0.6640 (m90) REVERT: D 195 ASN cc_start: 0.8831 (m-40) cc_final: 0.8568 (t0) REVERT: D 196 MET cc_start: 0.7233 (mmm) cc_final: 0.6723 (mmm) REVERT: D 205 GLU cc_start: 0.8478 (mp0) cc_final: 0.7610 (mp0) REVERT: D 223 ASP cc_start: 0.8463 (t70) cc_final: 0.8162 (t0) REVERT: D 265 THR cc_start: 0.8165 (m) cc_final: 0.7707 (p) REVERT: D 269 GLU cc_start: 0.5695 (pt0) cc_final: 0.5306 (pt0) REVERT: F 130 ARG cc_start: 0.7801 (mmp-170) cc_final: 0.7544 (mmp80) REVERT: F 134 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7725 (tm-30) REVERT: F 201 HIS cc_start: 0.7729 (m-70) cc_final: 0.7399 (m-70) REVERT: F 220 MET cc_start: 0.7873 (tpt) cc_final: 0.7318 (tpt) REVERT: G 62 TRP cc_start: 0.7148 (m-10) cc_final: 0.6870 (m-10) REVERT: G 65 ASP cc_start: 0.8507 (t0) cc_final: 0.8278 (t0) REVERT: G 85 TYR cc_start: 0.7393 (t80) cc_final: 0.7066 (t80) REVERT: G 127 TYR cc_start: 0.6877 (m-10) cc_final: 0.6623 (m-10) REVERT: G 141 ILE cc_start: 0.8270 (mt) cc_final: 0.7994 (tt) REVERT: G 205 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8667 (mt-10) REVERT: H 7 GLU cc_start: 0.8795 (pt0) cc_final: 0.8488 (pm20) REVERT: H 134 GLU cc_start: 0.8450 (mp0) cc_final: 0.8048 (tm-30) REVERT: H 138 ARG cc_start: 0.7323 (ttt180) cc_final: 0.7063 (tpt-90) REVERT: H 161 HIS cc_start: 0.7366 (m-70) cc_final: 0.6642 (m90) REVERT: H 195 ASN cc_start: 0.8831 (m-40) cc_final: 0.8564 (t0) REVERT: H 196 MET cc_start: 0.7239 (mmm) cc_final: 0.6724 (mmm) REVERT: H 205 GLU cc_start: 0.8481 (mp0) cc_final: 0.7612 (mp0) REVERT: H 223 ASP cc_start: 0.8468 (t70) cc_final: 0.8157 (t0) REVERT: H 265 THR cc_start: 0.8171 (m) cc_final: 0.7711 (p) REVERT: H 269 GLU cc_start: 0.5699 (pt0) cc_final: 0.5311 (pt0) outliers start: 16 outliers final: 12 residues processed: 262 average time/residue: 0.1483 time to fit residues: 59.7005 Evaluate side-chains 230 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 0.6980 chunk 154 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 155 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 180 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 195 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4098 r_free = 0.4098 target = 0.131379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095015 restraints weight = 39754.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095118 restraints weight = 20811.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095514 restraints weight = 15796.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096034 restraints weight = 13120.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096085 restraints weight = 11693.241| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19858 Z= 0.127 Angle : 0.560 8.494 27598 Z= 0.310 Chirality : 0.040 0.188 3002 Planarity : 0.004 0.040 3000 Dihedral : 22.107 83.333 3740 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.21 % Allowed : 9.77 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1936 helix: 1.58 (0.18), residues: 826 sheet: 0.47 (0.29), residues: 366 loop : -0.51 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.016 0.001 TYR G 77 PHE 0.016 0.001 PHE C 23 TRP 0.016 0.001 TRP B 208 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (19826) covalent geometry : angle 0.55548 / 0.31 (27584) hydrogen bonds : bond 0.03840 / 2.65 ( 960) hydrogen bonds : angle 5.22344 / 3.77 ( 2588) metal coordination : bond 0.00733 / 0.52 ( 32) metal coordination : angle 3.05521 / 1.44 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.694 Fit side-chains REVERT: B 130 ARG cc_start: 0.7876 (mmp-170) cc_final: 0.7644 (mmp80) REVERT: B 134 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 201 HIS cc_start: 0.7638 (m-70) cc_final: 0.7352 (m-70) REVERT: B 220 MET cc_start: 0.7798 (tpt) cc_final: 0.7342 (tpt) REVERT: C 62 TRP cc_start: 0.7032 (m-10) cc_final: 0.5972 (m-10) REVERT: C 65 ASP cc_start: 0.8611 (t0) cc_final: 0.8347 (t0) REVERT: C 85 TYR cc_start: 0.7428 (t80) cc_final: 0.7177 (t80) REVERT: C 113 MET cc_start: 0.6690 (mtt) cc_final: 0.6409 (mtm) REVERT: C 192 ASN cc_start: 0.6193 (m-40) cc_final: 0.5895 (m110) REVERT: C 205 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8656 (mt-10) REVERT: D 7 GLU cc_start: 0.8777 (pt0) cc_final: 0.8421 (pm20) REVERT: D 59 ARG cc_start: 0.7457 (mpp80) cc_final: 0.6965 (mpp80) REVERT: D 62 TRP cc_start: 0.7184 (m-10) cc_final: 0.6793 (m-10) REVERT: D 134 GLU cc_start: 0.8513 (mp0) cc_final: 0.8093 (tm-30) REVERT: D 196 MET cc_start: 0.7272 (mmm) cc_final: 0.6495 (mmm) REVERT: D 205 GLU cc_start: 0.8402 (mp0) cc_final: 0.7539 (mp0) REVERT: D 220 MET cc_start: 0.8979 (mmm) cc_final: 0.8700 (mmm) REVERT: D 223 ASP cc_start: 0.8399 (t70) cc_final: 0.8103 (t0) REVERT: D 265 THR cc_start: 0.8091 (m) cc_final: 0.7699 (p) REVERT: D 269 GLU cc_start: 0.5668 (pt0) cc_final: 0.5312 (pt0) REVERT: F 130 ARG cc_start: 0.7867 (mmp-170) cc_final: 0.7638 (mmp80) REVERT: F 134 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F 201 HIS cc_start: 0.7630 (m-70) cc_final: 0.7345 (m-70) REVERT: F 220 MET cc_start: 0.7795 (tpt) cc_final: 0.7346 (tpt) REVERT: G 62 TRP cc_start: 0.7035 (m-10) cc_final: 0.5980 (m-10) REVERT: G 65 ASP cc_start: 0.8609 (t0) cc_final: 0.8342 (t0) REVERT: G 85 TYR cc_start: 0.7430 (t80) cc_final: 0.7176 (t80) REVERT: G 113 MET cc_start: 0.6686 (mtt) cc_final: 0.6412 (mtm) REVERT: G 192 ASN cc_start: 0.6209 (m-40) cc_final: 0.5898 (m110) REVERT: G 205 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8651 (mt-10) REVERT: H 7 GLU cc_start: 0.8776 (pt0) cc_final: 0.8421 (pm20) REVERT: H 59 ARG cc_start: 0.7453 (mpp80) cc_final: 0.6957 (mpp80) REVERT: H 62 TRP cc_start: 0.7189 (m-10) cc_final: 0.6802 (m-10) REVERT: H 134 GLU cc_start: 0.8513 (mp0) cc_final: 0.8090 (tm-30) REVERT: H 196 MET cc_start: 0.7273 (mmm) cc_final: 0.6496 (mmm) REVERT: H 205 GLU cc_start: 0.8404 (mp0) cc_final: 0.7541 (mp0) REVERT: H 220 MET cc_start: 0.8974 (mmm) cc_final: 0.8698 (mmm) REVERT: H 223 ASP cc_start: 0.8400 (t70) cc_final: 0.8097 (t0) REVERT: H 265 THR cc_start: 0.8093 (m) cc_final: 0.7699 (p) REVERT: H 269 GLU cc_start: 0.5673 (pt0) cc_final: 0.5319 (pt0) outliers start: 20 outliers final: 10 residues processed: 246 average time/residue: 0.1456 time to fit residues: 56.1028 Evaluate side-chains 216 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 205 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN C 201 HIS D 162 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN G 201 HIS ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.130010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093885 restraints weight = 39805.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093395 restraints weight = 21541.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093605 restraints weight = 16565.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.094075 restraints weight = 14118.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094233 restraints weight = 13339.007| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19858 Z= 0.152 Angle : 0.552 6.470 27598 Z= 0.307 Chirality : 0.040 0.196 3002 Planarity : 0.004 0.036 3000 Dihedral : 22.185 81.925 3740 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.21 % Allowed : 11.22 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1936 helix: 1.66 (0.18), residues: 828 sheet: 0.47 (0.29), residues: 366 loop : -0.54 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 20 TYR 0.011 0.001 TYR H 242 PHE 0.012 0.001 PHE C 23 TRP 0.013 0.001 TRP B 208 HIS 0.015 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (19826) covalent geometry : angle 0.55010 / 0.31 (27584) hydrogen bonds : bond 0.03743 / 2.60 ( 960) hydrogen bonds : angle 5.06847 / 3.65 ( 2588) metal coordination : bond 0.00482 / 0.34 ( 32) metal coordination : angle 1.85493 / 0.91 ( 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 238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 201 HIS cc_start: 0.7570 (m-70) cc_final: 0.7331 (m-70) REVERT: B 220 MET cc_start: 0.7783 (tpt) cc_final: 0.7447 (mmm) REVERT: C 62 TRP cc_start: 0.7143 (m-10) cc_final: 0.6054 (m-10) REVERT: C 65 ASP cc_start: 0.8586 (t0) cc_final: 0.8324 (t0) REVERT: C 85 TYR cc_start: 0.7349 (t80) cc_final: 0.7140 (t80) REVERT: C 113 MET cc_start: 0.6603 (mtt) cc_final: 0.6368 (mtm) REVERT: C 205 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8580 (mt-10) REVERT: D 7 GLU cc_start: 0.8744 (pt0) cc_final: 0.8426 (pm20) REVERT: D 59 ARG cc_start: 0.7538 (mpp80) cc_final: 0.7016 (mpp80) REVERT: D 62 TRP cc_start: 0.7274 (m-10) cc_final: 0.6882 (m-10) REVERT: D 134 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: D 161 HIS cc_start: 0.7253 (m170) cc_final: 0.6980 (m90) REVERT: D 196 MET cc_start: 0.7311 (mmm) cc_final: 0.6397 (mmm) REVERT: D 205 GLU cc_start: 0.8590 (mp0) cc_final: 0.7736 (mp0) REVERT: D 220 MET cc_start: 0.8963 (mmm) cc_final: 0.8648 (mmm) REVERT: D 223 ASP cc_start: 0.8386 (t70) cc_final: 0.8148 (t0) REVERT: D 265 THR cc_start: 0.8205 (m) cc_final: 0.7879 (p) REVERT: D 269 GLU cc_start: 0.5692 (pt0) cc_final: 0.5312 (pt0) REVERT: F 134 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7767 (tm-30) REVERT: F 201 HIS cc_start: 0.7570 (m-70) cc_final: 0.7331 (m-70) REVERT: F 220 MET cc_start: 0.7775 (tpt) cc_final: 0.7445 (mmm) REVERT: G 62 TRP cc_start: 0.7148 (m-10) cc_final: 0.6069 (m-10) REVERT: G 65 ASP cc_start: 0.8587 (t0) cc_final: 0.8327 (t0) REVERT: G 85 TYR cc_start: 0.7353 (t80) cc_final: 0.7140 (t80) REVERT: G 113 MET cc_start: 0.6606 (mtt) cc_final: 0.6374 (mtm) REVERT: G 205 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8579 (mt-10) REVERT: H 7 GLU cc_start: 0.8742 (pt0) cc_final: 0.8428 (pm20) REVERT: H 59 ARG cc_start: 0.7535 (mpp80) cc_final: 0.7012 (mpp80) REVERT: H 62 TRP cc_start: 0.7279 (m-10) cc_final: 0.6891 (m-10) REVERT: H 134 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: H 161 HIS cc_start: 0.7257 (m170) cc_final: 0.6981 (m90) REVERT: H 196 MET cc_start: 0.7319 (mmm) cc_final: 0.6403 (mmm) REVERT: H 205 GLU cc_start: 0.8595 (mp0) cc_final: 0.7738 (mp0) REVERT: H 220 MET cc_start: 0.8958 (mmm) cc_final: 0.8645 (mmm) REVERT: H 223 ASP cc_start: 0.8384 (t70) cc_final: 0.8147 (t0) REVERT: H 265 THR cc_start: 0.8206 (m) cc_final: 0.7879 (p) REVERT: H 269 GLU cc_start: 0.5695 (pt0) cc_final: 0.5314 (pt0) outliers start: 20 outliers final: 16 residues processed: 234 average time/residue: 0.1441 time to fit residues: 52.4821 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 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 E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4056 r_free = 0.4056 target = 0.128415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093359 restraints weight = 39492.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091575 restraints weight = 23467.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092315 restraints weight = 18794.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.092620 restraints weight = 15028.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092740 restraints weight = 13817.632| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19858 Z= 0.175 Angle : 0.561 6.083 27598 Z= 0.312 Chirality : 0.041 0.183 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.259 84.147 3740 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 11.94 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1936 helix: 1.61 (0.18), residues: 830 sheet: 0.52 (0.29), residues: 374 loop : -0.58 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.012 0.001 TYR A 77 PHE 0.014 0.001 PHE C 23 TRP 0.013 0.001 TRP B 208 HIS 0.011 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (19826) covalent geometry : angle 0.55922 / 0.31 (27584) hydrogen bonds : bond 0.03748 / 2.60 ( 960) hydrogen bonds : angle 5.00933 / 3.60 ( 2588) metal coordination : bond 0.00732 / 0.51 ( 32) metal coordination : angle 1.79732 / 0.96 ( 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 246 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8577 (tp) cc_final: 0.8354 (tp) REVERT: C 65 ASP cc_start: 0.8582 (t0) cc_final: 0.8318 (t0) REVERT: C 169 ASN cc_start: 0.7020 (m-40) cc_final: 0.5957 (t0) REVERT: C 196 MET cc_start: 0.7433 (pmm) cc_final: 0.7205 (pmm) REVERT: C 205 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8597 (mt-10) REVERT: D 7 GLU cc_start: 0.8761 (pt0) cc_final: 0.8420 (pm20) REVERT: D 20 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.8035 (ptm160) REVERT: D 62 TRP cc_start: 0.7190 (m-10) cc_final: 0.6834 (m-10) REVERT: D 134 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: D 161 HIS cc_start: 0.7244 (m170) cc_final: 0.6927 (m90) REVERT: D 195 ASN cc_start: 0.8493 (t0) cc_final: 0.7874 (m110) REVERT: D 196 MET cc_start: 0.7416 (mmm) cc_final: 0.7071 (mmt) REVERT: D 205 GLU cc_start: 0.8425 (mp0) cc_final: 0.7538 (mp0) REVERT: D 220 MET cc_start: 0.8879 (mmm) cc_final: 0.8538 (mmm) REVERT: D 269 GLU cc_start: 0.6014 (pt0) cc_final: 0.5706 (pt0) REVERT: E 2 LEU cc_start: 0.8575 (tp) cc_final: 0.8350 (tp) REVERT: F 134 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7755 (tm-30) REVERT: G 65 ASP cc_start: 0.8587 (t0) cc_final: 0.8322 (t0) REVERT: G 169 ASN cc_start: 0.7008 (m-40) cc_final: 0.5946 (t0) REVERT: G 196 MET cc_start: 0.7421 (pmm) cc_final: 0.7196 (pmm) REVERT: G 205 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8597 (mt-10) REVERT: H 7 GLU cc_start: 0.8764 (pt0) cc_final: 0.8423 (pm20) REVERT: H 20 ARG cc_start: 0.8289 (ptm-80) cc_final: 0.8031 (ptm160) REVERT: H 62 TRP cc_start: 0.7192 (m-10) cc_final: 0.6834 (m-10) REVERT: H 134 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: H 161 HIS cc_start: 0.7247 (m170) cc_final: 0.6928 (m90) REVERT: H 195 ASN cc_start: 0.8489 (t0) cc_final: 0.7864 (m110) REVERT: H 196 MET cc_start: 0.7422 (mmm) cc_final: 0.7067 (mmt) REVERT: H 205 GLU cc_start: 0.8433 (mp0) cc_final: 0.7540 (mp0) REVERT: H 220 MET cc_start: 0.8872 (mmm) cc_final: 0.8529 (mmm) REVERT: H 269 GLU cc_start: 0.6014 (pt0) cc_final: 0.5704 (pt0) outliers start: 32 outliers final: 22 residues processed: 240 average time/residue: 0.1451 time to fit residues: 54.0484 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4187 r_free = 0.4187 target = 0.134341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098638 restraints weight = 39038.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097692 restraints weight = 21996.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098617 restraints weight = 15501.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098838 restraints weight = 12870.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098953 restraints weight = 11397.547| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19858 Z= 0.147 Angle : 0.557 7.672 27598 Z= 0.308 Chirality : 0.040 0.174 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.223 84.444 3740 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.69 % Allowed : 13.39 % Favored : 84.92 % 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: 0.87 (0.20), residues: 1936 helix: 1.67 (0.18), residues: 830 sheet: 0.46 (0.29), residues: 378 loop : -0.59 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 20 TYR 0.014 0.001 TYR E 77 PHE 0.017 0.001 PHE C 21 TRP 0.014 0.001 TRP F 208 HIS 0.007 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (19826) covalent geometry : angle 0.55472 / 0.31 (27584) hydrogen bonds : bond 0.03546 / 2.46 ( 960) hydrogen bonds : angle 4.92186 / 3.53 ( 2588) metal coordination : bond 0.00559 / 0.39 ( 32) metal coordination : angle 2.06112 / 1.05 ( 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 238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8619 (tp) cc_final: 0.8378 (tp) REVERT: B 220 MET cc_start: 0.7794 (mmm) cc_final: 0.7170 (mmm) REVERT: C 64 MET cc_start: 0.7922 (ttp) cc_final: 0.7314 (ttp) REVERT: C 65 ASP cc_start: 0.8664 (t0) cc_final: 0.8367 (t0) REVERT: C 169 ASN cc_start: 0.7030 (m-40) cc_final: 0.5988 (t0) REVERT: C 205 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8642 (mt-10) REVERT: D 7 GLU cc_start: 0.8827 (pt0) cc_final: 0.8424 (pm20) REVERT: D 20 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.8019 (ptm160) REVERT: D 62 TRP cc_start: 0.7058 (m-10) cc_final: 0.6738 (m-10) REVERT: D 134 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: D 161 HIS cc_start: 0.7168 (m170) cc_final: 0.6869 (m90) REVERT: D 171 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 195 ASN cc_start: 0.8564 (t0) cc_final: 0.7868 (m110) REVERT: D 196 MET cc_start: 0.7504 (mmm) cc_final: 0.7144 (mmt) REVERT: D 202 THR cc_start: 0.6152 (OUTLIER) cc_final: 0.5512 (p) REVERT: D 205 GLU cc_start: 0.8348 (mp0) cc_final: 0.7680 (mp0) REVERT: D 220 MET cc_start: 0.8899 (mmm) cc_final: 0.8370 (mmm) REVERT: D 269 GLU cc_start: 0.5993 (pt0) cc_final: 0.5568 (pt0) REVERT: E 2 LEU cc_start: 0.8617 (tp) cc_final: 0.8374 (tp) REVERT: F 134 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7835 (tm-30) REVERT: F 220 MET cc_start: 0.7787 (mmm) cc_final: 0.7165 (mmm) REVERT: G 64 MET cc_start: 0.7912 (ttp) cc_final: 0.7300 (ttp) REVERT: G 65 ASP cc_start: 0.8657 (t0) cc_final: 0.8360 (t0) REVERT: G 169 ASN cc_start: 0.7028 (m-40) cc_final: 0.5986 (t0) REVERT: G 205 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8639 (mt-10) REVERT: H 7 GLU cc_start: 0.8828 (pt0) cc_final: 0.8426 (pm20) REVERT: H 20 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.8012 (ptm160) REVERT: H 62 TRP cc_start: 0.7066 (m-10) cc_final: 0.6740 (m-10) REVERT: H 134 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: H 161 HIS cc_start: 0.7167 (m170) cc_final: 0.6866 (m90) REVERT: H 171 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8475 (mm) REVERT: H 195 ASN cc_start: 0.8558 (t0) cc_final: 0.7854 (m110) REVERT: H 196 MET cc_start: 0.7513 (mmm) cc_final: 0.7140 (mmt) REVERT: H 202 THR cc_start: 0.6169 (OUTLIER) cc_final: 0.5531 (p) REVERT: H 205 GLU cc_start: 0.8350 (mp0) cc_final: 0.7679 (mp0) REVERT: H 220 MET cc_start: 0.8893 (mmm) cc_final: 0.8365 (mmm) REVERT: H 269 GLU cc_start: 0.5995 (pt0) cc_final: 0.5572 (pt0) outliers start: 28 outliers final: 18 residues processed: 234 average time/residue: 0.1445 time to fit residues: 52.3215 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 199 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097954 restraints weight = 39384.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097130 restraints weight = 21175.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.098003 restraints weight = 15287.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098202 restraints weight = 12642.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098394 restraints weight = 11279.765| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19858 Z= 0.160 Angle : 0.565 6.302 27598 Z= 0.313 Chirality : 0.040 0.168 3002 Planarity : 0.004 0.036 3000 Dihedral : 22.248 84.168 3740 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.57 % Allowed : 14.84 % Favored : 83.59 % 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: 0.81 (0.20), residues: 1936 helix: 1.65 (0.18), residues: 832 sheet: 0.33 (0.29), residues: 380 loop : -0.61 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 20 TYR 0.015 0.001 TYR A 77 PHE 0.016 0.001 PHE C 21 TRP 0.015 0.001 TRP B 208 HIS 0.006 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (19826) covalent geometry : angle 0.56388 / 0.31 (27584) hydrogen bonds : bond 0.03557 / 2.47 ( 960) hydrogen bonds : angle 4.90439 / 3.51 ( 2588) metal coordination : bond 0.00597 / 0.41 ( 32) metal coordination : angle 1.78520 / 0.94 ( 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: 26 poor density : 204 time to evaluate : 0.726 Fit side-chains REVERT: A 2 LEU cc_start: 0.8520 (tp) cc_final: 0.8305 (tp) REVERT: B 177 TYR cc_start: 0.8170 (m-80) cc_final: 0.7964 (m-80) REVERT: C 65 ASP cc_start: 0.8804 (t0) cc_final: 0.8459 (t0) REVERT: C 169 ASN cc_start: 0.7012 (m-40) cc_final: 0.5998 (t0) REVERT: C 205 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8633 (mt-10) REVERT: D 7 GLU cc_start: 0.8812 (pt0) cc_final: 0.8387 (pm20) REVERT: D 62 TRP cc_start: 0.7067 (m-10) cc_final: 0.6730 (m-10) REVERT: D 134 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: D 161 HIS cc_start: 0.7233 (m170) cc_final: 0.6968 (m90) REVERT: D 195 ASN cc_start: 0.8609 (t0) cc_final: 0.7907 (m110) REVERT: D 196 MET cc_start: 0.7514 (mmm) cc_final: 0.7213 (mmt) REVERT: D 202 THR cc_start: 0.6153 (OUTLIER) cc_final: 0.5533 (p) REVERT: D 205 GLU cc_start: 0.8355 (mp0) cc_final: 0.7672 (mp0) REVERT: D 220 MET cc_start: 0.8874 (mmm) cc_final: 0.8291 (mmm) REVERT: D 269 GLU cc_start: 0.6014 (pt0) cc_final: 0.5661 (pt0) REVERT: E 2 LEU cc_start: 0.8522 (tp) cc_final: 0.8305 (tp) REVERT: F 134 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7847 (tm-30) REVERT: F 177 TYR cc_start: 0.8175 (m-80) cc_final: 0.7959 (m-80) REVERT: G 65 ASP cc_start: 0.8800 (t0) cc_final: 0.8455 (t0) REVERT: G 169 ASN cc_start: 0.7010 (m-40) cc_final: 0.5997 (t0) REVERT: G 205 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8628 (mt-10) REVERT: H 7 GLU cc_start: 0.8811 (pt0) cc_final: 0.8388 (pm20) REVERT: H 62 TRP cc_start: 0.7078 (m-10) cc_final: 0.6738 (m-10) REVERT: H 134 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: H 161 HIS cc_start: 0.7228 (m170) cc_final: 0.6963 (m90) REVERT: H 195 ASN cc_start: 0.8604 (t0) cc_final: 0.7908 (m110) REVERT: H 196 MET cc_start: 0.7500 (mmm) cc_final: 0.7182 (mmt) REVERT: H 202 THR cc_start: 0.6160 (OUTLIER) cc_final: 0.5533 (p) REVERT: H 205 GLU cc_start: 0.8359 (mp0) cc_final: 0.7675 (mp0) REVERT: H 220 MET cc_start: 0.8874 (mmm) cc_final: 0.8291 (mmm) REVERT: H 269 GLU cc_start: 0.6018 (pt0) cc_final: 0.5669 (pt0) outliers start: 26 outliers final: 16 residues processed: 226 average time/residue: 0.1469 time to fit residues: 51.6410 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 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 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 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: 3.9990 chunk 181 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 128 optimal weight: 0.0070 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4167 r_free = 0.4167 target = 0.132297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098400 restraints weight = 39260.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098251 restraints weight = 24313.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098533 restraints weight = 20047.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098770 restraints weight = 15518.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098988 restraints weight = 13801.752| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19858 Z= 0.177 Angle : 0.596 13.166 27598 Z= 0.324 Chirality : 0.041 0.167 3002 Planarity : 0.004 0.037 3000 Dihedral : 22.306 84.544 3740 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.45 % Allowed : 14.96 % Favored : 83.59 % 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: 0.81 (0.20), residues: 1936 helix: 1.66 (0.19), residues: 832 sheet: 0.36 (0.28), residues: 376 loop : -0.63 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.015 0.001 TYR A 77 PHE 0.014 0.001 PHE C 21 TRP 0.016 0.001 TRP E 208 HIS 0.007 0.001 HIS H 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (19826) covalent geometry : angle 0.59513 / 0.32 (27584) hydrogen bonds : bond 0.03599 / 2.50 ( 960) hydrogen bonds : angle 4.89191 / 3.50 ( 2588) metal coordination : bond 0.00735 / 0.50 ( 32) metal coordination : angle 1.75820 / 0.95 ( 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 238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.683 Fit side-chains REVERT: A 2 LEU cc_start: 0.8705 (tp) cc_final: 0.8477 (tp) REVERT: C 169 ASN cc_start: 0.6758 (m-40) cc_final: 0.5884 (t0) REVERT: C 205 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8517 (mt-10) REVERT: D 7 GLU cc_start: 0.8517 (pt0) cc_final: 0.8316 (pm20) REVERT: D 62 TRP cc_start: 0.7535 (m-10) cc_final: 0.7130 (m-10) REVERT: D 134 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: D 159 ARG cc_start: 0.8812 (tpt90) cc_final: 0.8508 (tpt90) REVERT: D 161 HIS cc_start: 0.7368 (m170) cc_final: 0.7115 (m90) REVERT: D 171 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8553 (mm) REVERT: D 195 ASN cc_start: 0.8425 (t0) cc_final: 0.7921 (m110) REVERT: D 196 MET cc_start: 0.7309 (mmm) cc_final: 0.6913 (mmt) REVERT: D 205 GLU cc_start: 0.8380 (mp0) cc_final: 0.7935 (mp0) REVERT: D 220 MET cc_start: 0.8837 (mmm) cc_final: 0.8327 (mmm) REVERT: D 269 GLU cc_start: 0.6042 (pt0) cc_final: 0.5682 (pt0) REVERT: E 2 LEU cc_start: 0.8704 (tp) cc_final: 0.8473 (tp) REVERT: F 134 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7805 (tm-30) REVERT: G 169 ASN cc_start: 0.6765 (m-40) cc_final: 0.5890 (t0) REVERT: G 205 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 7 GLU cc_start: 0.8511 (pt0) cc_final: 0.8311 (pm20) REVERT: H 62 TRP cc_start: 0.7526 (m-10) cc_final: 0.7120 (m-10) REVERT: H 134 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: H 159 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8521 (tpt90) REVERT: H 161 HIS cc_start: 0.7363 (m170) cc_final: 0.7110 (m90) REVERT: H 171 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8551 (mm) REVERT: H 195 ASN cc_start: 0.8424 (t0) cc_final: 0.7919 (m110) REVERT: H 196 MET cc_start: 0.7313 (mmm) cc_final: 0.6914 (mmt) REVERT: H 205 GLU cc_start: 0.8380 (mp0) cc_final: 0.7934 (mp0) REVERT: H 220 MET cc_start: 0.8836 (mmm) cc_final: 0.8326 (mmm) REVERT: H 269 GLU cc_start: 0.6045 (pt0) cc_final: 0.5685 (pt0) outliers start: 24 outliers final: 16 residues processed: 232 average time/residue: 0.1442 time to fit residues: 52.1050 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 96 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097338 restraints weight = 38872.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097808 restraints weight = 19284.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098823 restraints weight = 12597.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098902 restraints weight = 10693.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099059 restraints weight = 9853.985| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2578 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= 0.131 Angle : 0.577 8.125 27598 Z= 0.316 Chirality : 0.040 0.141 3002 Planarity : 0.004 0.036 3000 Dihedral : 22.217 83.933 3740 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.57 % Allowed : 15.56 % 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: 0.88 (0.20), residues: 1936 helix: 1.69 (0.19), residues: 832 sheet: 0.28 (0.28), residues: 384 loop : -0.50 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.013 0.001 TYR G 177 PHE 0.016 0.001 PHE G 21 TRP 0.018 0.001 TRP E 208 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (19826) covalent geometry : angle 0.57435 / 0.32 (27584) hydrogen bonds : bond 0.03373 / 2.32 ( 960) hydrogen bonds : angle 4.82408 / 3.46 ( 2588) metal coordination : bond 0.00624 / 0.43 ( 32) metal coordination : angle 2.29503 / 1.20 ( 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 232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.688 Fit side-chains REVERT: A 2 LEU cc_start: 0.8542 (tp) cc_final: 0.8303 (tp) REVERT: C 85 TYR cc_start: 0.6979 (t80) cc_final: 0.6572 (t80) REVERT: C 169 ASN cc_start: 0.7017 (m-40) cc_final: 0.6037 (t0) REVERT: C 205 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8678 (mt-10) REVERT: D 7 GLU cc_start: 0.8888 (pt0) cc_final: 0.8374 (pm20) REVERT: D 62 TRP cc_start: 0.6805 (m-10) cc_final: 0.6449 (m-10) REVERT: D 134 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: D 161 HIS cc_start: 0.7193 (m170) cc_final: 0.6956 (m90) REVERT: D 171 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8444 (mm) REVERT: D 195 ASN cc_start: 0.8568 (t0) cc_final: 0.7728 (m110) REVERT: D 205 GLU cc_start: 0.8399 (mp0) cc_final: 0.7659 (mp0) REVERT: D 220 MET cc_start: 0.8850 (mmm) cc_final: 0.8193 (mmm) REVERT: D 269 GLU cc_start: 0.6011 (pt0) cc_final: 0.5661 (pt0) REVERT: E 2 LEU cc_start: 0.8547 (tp) cc_final: 0.8303 (tp) REVERT: F 134 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7846 (tm-30) REVERT: G 85 TYR cc_start: 0.6984 (t80) cc_final: 0.6577 (t80) REVERT: G 169 ASN cc_start: 0.7011 (m-40) cc_final: 0.6034 (t0) REVERT: G 205 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8676 (mt-10) REVERT: H 7 GLU cc_start: 0.8887 (pt0) cc_final: 0.8374 (pm20) REVERT: H 62 TRP cc_start: 0.6823 (m-10) cc_final: 0.6464 (m-10) REVERT: H 134 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: H 161 HIS cc_start: 0.7196 (m170) cc_final: 0.6960 (m90) REVERT: H 171 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (mm) REVERT: H 195 ASN cc_start: 0.8566 (t0) cc_final: 0.7726 (m110) REVERT: H 205 GLU cc_start: 0.8403 (mp0) cc_final: 0.7664 (mp0) REVERT: H 220 MET cc_start: 0.8846 (mmm) cc_final: 0.8192 (mmm) REVERT: H 269 GLU cc_start: 0.6011 (pt0) cc_final: 0.5661 (pt0) outliers start: 26 outliers final: 16 residues processed: 228 average time/residue: 0.1442 time to fit residues: 50.8163 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.134442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.097883 restraints weight = 39057.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098678 restraints weight = 19192.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099415 restraints weight = 12121.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.099791 restraints weight = 10550.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099941 restraints weight = 9774.996| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2650 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= 0.124 Angle : 0.563 7.974 27598 Z= 0.309 Chirality : 0.039 0.134 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.194 81.981 3740 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.21 % Allowed : 16.10 % Favored : 82.69 % 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: 0.92 (0.20), residues: 1936 helix: 1.72 (0.19), residues: 832 sheet: 0.25 (0.28), residues: 398 loop : -0.44 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 159 TYR 0.010 0.001 TYR A 77 PHE 0.016 0.001 PHE G 21 TRP 0.020 0.001 TRP E 208 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (19826) covalent geometry : angle 0.56092 / 0.31 (27584) hydrogen bonds : bond 0.03260 / 2.25 ( 960) hydrogen bonds : angle 4.75222 / 3.41 ( 2588) metal coordination : bond 0.00705 / 0.49 ( 32) metal coordination : angle 2.41580 / 1.27 ( 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 228 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.663 Fit side-chains REVERT: A 2 LEU cc_start: 0.8513 (tp) cc_final: 0.8260 (tp) REVERT: B 220 MET cc_start: 0.7880 (mmm) cc_final: 0.7492 (mmm) REVERT: C 85 TYR cc_start: 0.7033 (t80) cc_final: 0.6655 (t80) REVERT: C 169 ASN cc_start: 0.6968 (m-40) cc_final: 0.6021 (t0) REVERT: C 205 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8659 (mt-10) REVERT: D 7 GLU cc_start: 0.8877 (pt0) cc_final: 0.8332 (pm20) REVERT: D 62 TRP cc_start: 0.6831 (m-10) cc_final: 0.6522 (m-10) REVERT: D 134 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: D 171 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8429 (mm) REVERT: D 195 ASN cc_start: 0.8607 (t0) cc_final: 0.7691 (m110) REVERT: D 196 MET cc_start: 0.6594 (mmt) cc_final: 0.5844 (mmm) REVERT: D 205 GLU cc_start: 0.8401 (mp0) cc_final: 0.7620 (mp0) REVERT: D 220 MET cc_start: 0.8847 (mmm) cc_final: 0.8179 (mmm) REVERT: D 251 GLU cc_start: 0.7473 (tp30) cc_final: 0.7217 (tp30) REVERT: D 269 GLU cc_start: 0.5937 (pt0) cc_final: 0.5578 (pt0) REVERT: E 2 LEU cc_start: 0.8516 (tp) cc_final: 0.8262 (tp) REVERT: F 134 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7829 (tm-30) REVERT: F 220 MET cc_start: 0.7876 (mmm) cc_final: 0.7491 (mmm) REVERT: G 85 TYR cc_start: 0.7039 (t80) cc_final: 0.6658 (t80) REVERT: G 169 ASN cc_start: 0.6962 (m-40) cc_final: 0.6016 (t0) REVERT: G 205 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8656 (mt-10) REVERT: H 7 GLU cc_start: 0.8876 (pt0) cc_final: 0.8331 (pm20) REVERT: H 62 TRP cc_start: 0.6853 (m-10) cc_final: 0.6539 (m-10) REVERT: H 134 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: H 171 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (mm) REVERT: H 195 ASN cc_start: 0.8601 (t0) cc_final: 0.7690 (m110) REVERT: H 196 MET cc_start: 0.6600 (mmt) cc_final: 0.5845 (mmm) REVERT: H 205 GLU cc_start: 0.8404 (mp0) cc_final: 0.7625 (mp0) REVERT: H 220 MET cc_start: 0.8841 (mmm) cc_final: 0.8175 (mmm) REVERT: H 251 GLU cc_start: 0.7472 (tp30) cc_final: 0.7219 (tp30) REVERT: H 269 GLU cc_start: 0.5940 (pt0) cc_final: 0.5580 (pt0) outliers start: 20 outliers final: 16 residues processed: 224 average time/residue: 0.1448 time to fit residues: 50.2187 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 53 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 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 = 0.4167 r_free = 0.4167 target = 0.132097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098357 restraints weight = 39071.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098673 restraints weight = 24259.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098820 restraints weight = 19371.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.099072 restraints weight = 14685.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099272 restraints weight = 13317.845| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2752 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= 0.187 Angle : 0.600 7.513 27598 Z= 0.327 Chirality : 0.041 0.152 3002 Planarity : 0.004 0.038 3000 Dihedral : 22.324 82.770 3740 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.97 % Allowed : 16.47 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1936 helix: 1.69 (0.19), residues: 832 sheet: 0.20 (0.28), residues: 384 loop : -0.51 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 130 TYR 0.015 0.001 TYR E 77 PHE 0.013 0.001 PHE B 88 TRP 0.020 0.001 TRP E 208 HIS 0.006 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (19826) covalent geometry : angle 0.59927 / 0.33 (27584) hydrogen bonds : bond 0.03640 / 2.52 ( 960) hydrogen bonds : angle 4.76763 / 3.42 ( 2588) metal coordination : bond 0.00845 / 0.58 ( 32) metal coordination : angle 1.58793 / 0.85 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.94 seconds wall clock time: 52 minutes 39.85 seconds (3159.85 seconds total)