Starting phenix.real_space_refine on Mon Jun 16 17:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_26737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_26737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_26737.map" model { file = "/net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_26737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usf_26737/06_2025/7usf_26737.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: G, F, N, E, M, H, L Time building chain proxies: 12.87, per 1000 atoms: 0.68 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: 5.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 8.74 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: 9.23 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5270 1.34 - 1.45: 4410 1.45 - 1.57: 9746 1.57 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19826 Sorted by residual: bond pdb=" C THR E 121 " pdb=" N ASP E 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C THR A 121 " pdb=" N ASP A 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C ILE B 147 " pdb=" N PRO B 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" C ILE F 147 " pdb=" N PRO F 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" CB ASN C 123 " pdb=" CG ASN C 123 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 19821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27170 2.05 - 4.10: 392 4.10 - 6.15: 18 6.15 - 8.20: 2 8.20 - 10.25: 2 Bond angle restraints: 27584 Sorted by residual: angle pdb=" N THR C 226 " pdb=" CA THR C 226 " pdb=" C THR C 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N THR G 226 " pdb=" CA THR G 226 " pdb=" C THR G 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N VAL H 194 " pdb=" CA VAL H 194 " pdb=" C VAL H 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N VAL D 194 " pdb=" CA VAL D 194 " pdb=" C VAL D 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N GLY F 209 " pdb=" CA GLY F 209 " pdb=" C GLY F 209 " ideal model delta sigma weight residual 112.34 118.68 -6.34 2.04e+00 2.40e-01 9.66e+00 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9380 17.97 - 35.93: 1096 35.93 - 53.90: 586 53.90 - 71.87: 160 71.87 - 89.83: 12 Dihedral angle restraints: 11234 sinusoidal: 5438 harmonic: 5796 Sorted by residual: dihedral pdb=" CA TRP H 139 " pdb=" C TRP H 139 " pdb=" N LYS H 140 " pdb=" CA LYS H 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP D 139 " pdb=" C TRP D 139 " pdb=" N LYS D 140 " pdb=" CA LYS D 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY B 209 " pdb=" C GLY B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 11231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2162 0.036 - 0.071: 622 0.071 - 0.107: 176 0.107 - 0.143: 36 0.143 - 0.178: 6 Chirality restraints: 3002 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA TRP D 139 " pdb=" N TRP D 139 " pdb=" C TRP D 139 " pdb=" CB TRP D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2999 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN G 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN G 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA G 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN C 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN C 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 139 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.29e+00 pdb=" CG TRP D 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 139 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 139 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 126 2.59 - 3.17: 15458 3.17 - 3.75: 32720 3.75 - 4.32: 43088 4.32 - 4.90: 68437 Nonbonded interactions: 159829 Sorted by model distance: nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.017 3.040 nonbonded pdb=" OG1 THR D 202 " pdb=" OE1 GLU D 205 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASP A 65 " pdb="CA CA A 501 " model vdw 2.209 2.510 nonbonded pdb=" OD1 ASP E 65 " pdb="CA CA E 501 " model vdw 2.209 2.510 nonbonded pdb=" OH TYR C 242 " pdb=" OP1 DG L 10 " model vdw 2.219 3.040 ... (remaining 159824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } 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: 122.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.220 Process input model: 58.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19858 Z= 0.143 Angle : 0.600 20.278 27598 Z= 0.322 Chirality : 0.038 0.178 3002 Planarity : 0.004 0.052 3000 Dihedral : 19.616 89.833 7458 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (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 TRP 0.041 0.002 TRP D 139 HIS 0.012 0.001 HIS H 161 PHE 0.018 0.001 PHE G 88 TYR 0.015 0.001 TYR H 127 ARG 0.004 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.13779 ( 960) hydrogen bonds : angle 6.48990 ( 2588) metal coordination : bond 0.01488 ( 32) metal coordination : angle 10.38485 ( 14) covalent geometry : bond 0.00291 (19826) covalent geometry : angle 0.55285 (27584) *********************** 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 : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8452 (mmm) cc_final: 0.8179 (mmm) REVERT: A 244 CYS cc_start: 0.8664 (t) cc_final: 0.8120 (t) REVERT: B 130 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7631 (mmp80) REVERT: B 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7891 (m-70) REVERT: B 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6994 (tpt) REVERT: B 242 TYR cc_start: 0.8140 (m-10) cc_final: 0.7904 (m-10) REVERT: B 254 ILE cc_start: 0.8543 (mt) cc_final: 0.8316 (tt) REVERT: C 64 MET cc_start: 0.7830 (ttp) cc_final: 0.7601 (ttm) REVERT: C 65 ASP cc_start: 0.8305 (t0) cc_final: 0.8025 (t0) REVERT: C 85 TYR cc_start: 0.7379 (t80) cc_final: 0.7020 (t80) REVERT: C 110 PHE cc_start: 0.8497 (m-10) cc_final: 0.7893 (m-10) REVERT: C 196 MET cc_start: 0.7994 (ptp) cc_final: 0.6728 (ptp) REVERT: C 205 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 7 GLU cc_start: 0.8884 (pt0) cc_final: 0.8365 (pp20) REVERT: D 62 TRP cc_start: 0.7266 (m-10) cc_final: 0.6954 (m-10) REVERT: D 134 GLU cc_start: 0.8224 (mp0) cc_final: 0.7979 (mp0) REVERT: D 138 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7062 (tpt-90) REVERT: D 159 ARG cc_start: 0.9011 (tmt-80) cc_final: 0.8572 (tpt90) REVERT: D 161 HIS cc_start: 0.7013 (m-70) cc_final: 0.6615 (m90) REVERT: D 196 MET cc_start: 0.7355 (mmm) cc_final: 0.6792 (mmm) REVERT: D 205 GLU cc_start: 0.8167 (mp0) cc_final: 0.7170 (mp0) REVERT: E 64 MET cc_start: 0.8792 (ttm) cc_final: 0.8592 (ttm) REVERT: E 218 MET cc_start: 0.8460 (mmm) cc_final: 0.8186 (mmm) REVERT: E 244 CYS cc_start: 0.8671 (t) cc_final: 0.8128 (t) REVERT: F 130 ARG cc_start: 0.7952 (mmp-170) cc_final: 0.7632 (mmp80) REVERT: F 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7890 (m-70) REVERT: F 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6992 (tpt) REVERT: F 242 TYR cc_start: 0.8139 (m-10) cc_final: 0.7899 (m-10) REVERT: F 254 ILE cc_start: 0.8547 (mt) cc_final: 0.8321 (tt) REVERT: G 64 MET cc_start: 0.7824 (ttp) cc_final: 0.7598 (ttm) REVERT: G 65 ASP cc_start: 0.8301 (t0) cc_final: 0.8016 (t0) REVERT: G 85 TYR cc_start: 0.7383 (t80) cc_final: 0.7019 (t80) REVERT: G 110 PHE cc_start: 0.8496 (m-10) cc_final: 0.7891 (m-10) REVERT: G 196 MET cc_start: 0.8001 (ptp) cc_final: 0.6738 (ptp) REVERT: G 205 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8671 (mt-10) REVERT: H 7 GLU cc_start: 0.8882 (pt0) cc_final: 0.8364 (pp20) REVERT: H 62 TRP cc_start: 0.7268 (m-10) cc_final: 0.6955 (m-10) REVERT: H 134 GLU cc_start: 0.8223 (mp0) cc_final: 0.7977 (mp0) REVERT: H 138 ARG cc_start: 0.7335 (ttt180) cc_final: 0.7065 (tpt-90) REVERT: H 159 ARG cc_start: 0.9012 (tmt-80) cc_final: 0.8575 (tpt90) REVERT: H 161 HIS cc_start: 0.7012 (m-70) cc_final: 0.6617 (m90) REVERT: H 196 MET cc_start: 0.7356 (mmm) cc_final: 0.6794 (mmm) REVERT: H 205 GLU cc_start: 0.8172 (mp0) cc_final: 0.7173 (mp0) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.3144 time to fit residues: 151.1694 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 : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS C 192 ASN C 201 HIS ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS G 192 ASN G 201 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.130647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095297 restraints weight = 39334.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095749 restraints weight = 27295.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095906 restraints weight = 20334.803| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19858 Z= 0.287 Angle : 0.643 7.594 27598 Z= 0.354 Chirality : 0.043 0.139 3002 Planarity : 0.005 0.043 3000 Dihedral : 22.126 87.674 3740 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.45 % Allowed : 9.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1936 helix: 1.27 (0.18), residues: 818 sheet: 0.53 (0.29), residues: 360 loop : -0.48 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 208 HIS 0.009 0.002 HIS E 9 PHE 0.017 0.002 PHE C 88 TYR 0.018 0.002 TYR H 242 ARG 0.004 0.001 ARG H 20 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 960) hydrogen bonds : angle 5.38277 ( 2588) metal coordination : bond 0.01353 ( 32) metal coordination : angle 2.45892 ( 14) covalent geometry : bond 0.00659 (19826) covalent geometry : angle 0.64097 (27584) *********************** 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 272 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 1.882 Fit side-chains REVERT: B 3 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 130 ARG cc_start: 0.7689 (mmp-170) cc_final: 0.7477 (mmp80) REVERT: C 65 ASP cc_start: 0.8606 (t70) cc_final: 0.8349 (t0) REVERT: C 205 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8494 (mt-10) REVERT: D 20 ARG cc_start: 0.8398 (ptm-80) cc_final: 0.8182 (ptm-80) REVERT: D 134 GLU cc_start: 0.8330 (mp0) cc_final: 0.7994 (tm-30) REVERT: D 161 HIS cc_start: 0.7236 (m-70) cc_final: 0.6432 (m90) REVERT: D 195 ASN cc_start: 0.8628 (m-40) cc_final: 0.8185 (t0) REVERT: D 196 MET cc_start: 0.7177 (mmm) cc_final: 0.6613 (mmm) REVERT: D 205 GLU cc_start: 0.8260 (mp0) cc_final: 0.7247 (mp0) REVERT: D 220 MET cc_start: 0.8959 (mmm) cc_final: 0.8729 (mmm) REVERT: D 223 ASP cc_start: 0.8417 (t70) cc_final: 0.8202 (t0) REVERT: D 265 THR cc_start: 0.8305 (m) cc_final: 0.7911 (p) REVERT: D 269 GLU cc_start: 0.5989 (pt0) cc_final: 0.5752 (pt0) REVERT: F 3 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7017 (mm-30) REVERT: F 130 ARG cc_start: 0.7684 (mmp-170) cc_final: 0.7472 (mmp80) REVERT: G 65 ASP cc_start: 0.8608 (t70) cc_final: 0.8350 (t0) REVERT: G 205 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8492 (mt-10) REVERT: H 20 ARG cc_start: 0.8399 (ptm-80) cc_final: 0.8184 (ptm-80) REVERT: H 134 GLU cc_start: 0.8328 (mp0) cc_final: 0.7991 (tm-30) REVERT: H 161 HIS cc_start: 0.7237 (m-70) cc_final: 0.6425 (m90) REVERT: H 195 ASN cc_start: 0.8628 (m-40) cc_final: 0.8183 (t0) REVERT: H 196 MET cc_start: 0.7178 (mmm) cc_final: 0.6613 (mmm) REVERT: H 205 GLU cc_start: 0.8256 (mp0) cc_final: 0.7249 (mp0) REVERT: H 220 MET cc_start: 0.8953 (mmm) cc_final: 0.8730 (mmm) REVERT: H 223 ASP cc_start: 0.8420 (t70) cc_final: 0.8198 (t0) REVERT: H 265 THR cc_start: 0.8302 (m) cc_final: 0.7909 (p) REVERT: H 269 GLU cc_start: 0.5991 (pt0) cc_final: 0.5754 (pt0) outliers start: 24 outliers final: 14 residues processed: 260 average time/residue: 0.3081 time to fit residues: 122.5501 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 46 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 178 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN C 161 HIS ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN E 52 ASN G 161 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.132292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096812 restraints weight = 39048.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095863 restraints weight = 22681.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096452 restraints weight = 17601.369| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19858 Z= 0.175 Angle : 0.559 7.565 27598 Z= 0.306 Chirality : 0.039 0.134 3002 Planarity : 0.004 0.038 3000 Dihedral : 21.907 85.875 3740 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.47 % Allowed : 10.80 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1936 helix: 1.44 (0.18), residues: 820 sheet: 0.51 (0.29), residues: 372 loop : -0.55 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 208 HIS 0.006 0.001 HIS H 161 PHE 0.013 0.001 PHE G 23 TYR 0.016 0.001 TYR G 77 ARG 0.003 0.000 ARG H 20 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 960) hydrogen bonds : angle 5.10692 ( 2588) metal coordination : bond 0.00796 ( 32) metal coordination : angle 2.56249 ( 14) covalent geometry : bond 0.00397 (19826) covalent geometry : angle 0.55660 (27584) *********************** 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 263 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TRP cc_start: 0.7343 (m-10) cc_final: 0.6393 (m-10) REVERT: C 65 ASP cc_start: 0.8553 (t70) cc_final: 0.8289 (t0) REVERT: C 169 ASN cc_start: 0.6890 (m-40) cc_final: 0.5908 (t0) REVERT: C 205 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8557 (mt-10) REVERT: D 134 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: D 161 HIS cc_start: 0.7280 (m-70) cc_final: 0.6987 (m90) REVERT: D 196 MET cc_start: 0.7333 (mmm) cc_final: 0.6338 (mmm) REVERT: D 205 GLU cc_start: 0.8258 (mp0) cc_final: 0.7266 (mp0) REVERT: D 220 MET cc_start: 0.8942 (mmm) cc_final: 0.8286 (mmm) REVERT: D 223 ASP cc_start: 0.8523 (t70) cc_final: 0.8233 (t0) REVERT: D 269 GLU cc_start: 0.6069 (pt0) cc_final: 0.5766 (pt0) REVERT: G 62 TRP cc_start: 0.7347 (m-10) cc_final: 0.6399 (m-10) REVERT: G 65 ASP cc_start: 0.8565 (t70) cc_final: 0.8297 (t0) REVERT: G 169 ASN cc_start: 0.6899 (m-40) cc_final: 0.5913 (t0) REVERT: G 205 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8555 (mt-10) REVERT: H 134 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: H 161 HIS cc_start: 0.7277 (m-70) cc_final: 0.6987 (m90) REVERT: H 195 ASN cc_start: 0.8698 (m-40) cc_final: 0.8244 (t0) REVERT: H 196 MET cc_start: 0.7330 (mmm) cc_final: 0.6320 (mmm) REVERT: H 205 GLU cc_start: 0.8266 (mp0) cc_final: 0.7269 (mp0) REVERT: H 220 MET cc_start: 0.8936 (mmm) cc_final: 0.8289 (mmm) REVERT: H 223 ASP cc_start: 0.8517 (t70) cc_final: 0.8232 (t0) REVERT: H 269 GLU cc_start: 0.6071 (pt0) cc_final: 0.5768 (pt0) outliers start: 41 outliers final: 22 residues processed: 246 average time/residue: 0.3059 time to fit residues: 115.3811 Evaluate side-chains 232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 99 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN C 29 GLN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN G 29 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098145 restraints weight = 39122.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098466 restraints weight = 25104.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098517 restraints weight = 18942.959| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19858 Z= 0.181 Angle : 0.558 8.372 27598 Z= 0.304 Chirality : 0.039 0.144 3002 Planarity : 0.004 0.034 3000 Dihedral : 21.963 85.673 3740 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.53 % Allowed : 12.18 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1936 helix: 1.54 (0.19), residues: 822 sheet: 0.59 (0.29), residues: 360 loop : -0.56 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 208 HIS 0.005 0.001 HIS B 182 PHE 0.011 0.001 PHE G 23 TYR 0.014 0.001 TYR E 77 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 960) hydrogen bonds : angle 5.03611 ( 2588) metal coordination : bond 0.00777 ( 32) metal coordination : angle 2.20336 ( 14) covalent geometry : bond 0.00412 (19826) covalent geometry : angle 0.55602 (27584) *********************** 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 274 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7177 (mm-30) REVERT: B 3 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 220 MET cc_start: 0.7765 (mmm) cc_final: 0.7540 (mmm) REVERT: C 62 TRP cc_start: 0.7315 (m-10) cc_final: 0.5968 (m-10) REVERT: C 65 ASP cc_start: 0.8623 (t70) cc_final: 0.8401 (t0) REVERT: C 113 MET cc_start: 0.6468 (mtm) cc_final: 0.5926 (mtp) REVERT: C 169 ASN cc_start: 0.6638 (m-40) cc_final: 0.5875 (t0) REVERT: C 205 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8468 (mt-10) REVERT: D 134 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: D 196 MET cc_start: 0.7276 (mmm) cc_final: 0.6502 (mmm) REVERT: D 205 GLU cc_start: 0.8271 (mp0) cc_final: 0.7507 (mp0) REVERT: D 223 ASP cc_start: 0.8469 (t70) cc_final: 0.8263 (t0) REVERT: D 269 GLU cc_start: 0.6088 (pt0) cc_final: 0.5718 (pt0) REVERT: E 28 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7179 (mm-30) REVERT: F 3 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6785 (mm-30) REVERT: F 220 MET cc_start: 0.7757 (mmm) cc_final: 0.7535 (mmm) REVERT: G 62 TRP cc_start: 0.7307 (m-10) cc_final: 0.5961 (m-10) REVERT: G 65 ASP cc_start: 0.8629 (t70) cc_final: 0.8404 (t0) REVERT: G 113 MET cc_start: 0.6473 (mtm) cc_final: 0.5923 (mtp) REVERT: G 169 ASN cc_start: 0.6632 (m-40) cc_final: 0.5872 (t0) REVERT: G 205 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8466 (mt-10) REVERT: H 134 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: H 195 ASN cc_start: 0.8487 (m-40) cc_final: 0.8148 (t0) REVERT: H 196 MET cc_start: 0.7191 (mmm) cc_final: 0.6361 (mmm) REVERT: H 205 GLU cc_start: 0.8273 (mp0) cc_final: 0.7512 (mp0) REVERT: H 223 ASP cc_start: 0.8462 (t70) cc_final: 0.8259 (t0) REVERT: H 269 GLU cc_start: 0.6095 (pt0) cc_final: 0.5728 (pt0) outliers start: 42 outliers final: 19 residues processed: 264 average time/residue: 0.3038 time to fit residues: 123.0900 Evaluate side-chains 231 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.0980 chunk 193 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 157 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.132520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099001 restraints weight = 39228.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099007 restraints weight = 25561.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099214 restraints weight = 21049.084| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19858 Z= 0.173 Angle : 0.558 9.115 27598 Z= 0.304 Chirality : 0.039 0.132 3002 Planarity : 0.004 0.035 3000 Dihedral : 21.975 85.718 3740 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.11 % Allowed : 13.87 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1936 helix: 1.58 (0.19), residues: 822 sheet: 0.62 (0.29), residues: 360 loop : -0.63 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 208 HIS 0.016 0.001 HIS H 161 PHE 0.012 0.001 PHE G 23 TYR 0.010 0.001 TYR A 77 ARG 0.003 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 960) hydrogen bonds : angle 4.96591 ( 2588) metal coordination : bond 0.00750 ( 32) metal coordination : angle 2.11119 ( 14) covalent geometry : bond 0.00392 (19826) covalent geometry : angle 0.55578 (27584) *********************** 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 263 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8300 (mmm) cc_final: 0.8088 (mmm) REVERT: C 85 TYR cc_start: 0.6843 (t80) cc_final: 0.6458 (t80) REVERT: C 169 ASN cc_start: 0.6334 (m-40) cc_final: 0.5890 (t0) REVERT: C 205 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8457 (mt-10) REVERT: D 62 TRP cc_start: 0.7695 (m-10) cc_final: 0.7332 (m-10) REVERT: D 134 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: D 161 HIS cc_start: 0.7107 (m170) cc_final: 0.6737 (m90) REVERT: D 196 MET cc_start: 0.7071 (mmm) cc_final: 0.6445 (mmm) REVERT: D 205 GLU cc_start: 0.8329 (mp0) cc_final: 0.7912 (mp0) REVERT: D 220 MET cc_start: 0.8748 (mmm) cc_final: 0.8080 (mmm) REVERT: D 251 GLU cc_start: 0.7546 (tp30) cc_final: 0.7109 (tp30) REVERT: D 269 GLU cc_start: 0.6094 (pt0) cc_final: 0.5807 (pt0) REVERT: E 218 MET cc_start: 0.8296 (mmm) cc_final: 0.8088 (mmm) REVERT: G 85 TYR cc_start: 0.6826 (t80) cc_final: 0.6440 (t80) REVERT: G 169 ASN cc_start: 0.6340 (m-40) cc_final: 0.5895 (t0) REVERT: G 205 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8449 (mt-10) REVERT: H 62 TRP cc_start: 0.7692 (m-10) cc_final: 0.7327 (m-10) REVERT: H 134 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: H 161 HIS cc_start: 0.7090 (m170) cc_final: 0.6721 (m90) REVERT: H 195 ASN cc_start: 0.8579 (m-40) cc_final: 0.8267 (t0) REVERT: H 196 MET cc_start: 0.7001 (mmm) cc_final: 0.6459 (mmm) REVERT: H 205 GLU cc_start: 0.8333 (mp0) cc_final: 0.7917 (mp0) REVERT: H 220 MET cc_start: 0.8743 (mmm) cc_final: 0.8077 (mmm) REVERT: H 251 GLU cc_start: 0.7544 (tp30) cc_final: 0.7112 (tp30) REVERT: H 269 GLU cc_start: 0.6103 (pt0) cc_final: 0.5818 (pt0) outliers start: 35 outliers final: 23 residues processed: 255 average time/residue: 0.2990 time to fit residues: 117.5120 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 8 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 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 = 0.4136 r_free = 0.4136 target = 0.130753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095318 restraints weight = 39459.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093969 restraints weight = 23069.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094488 restraints weight = 18014.830| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19858 Z= 0.213 Angle : 0.589 7.557 27598 Z= 0.321 Chirality : 0.040 0.134 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.145 87.273 3740 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.87 % Allowed : 16.16 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1936 helix: 1.49 (0.18), residues: 822 sheet: 0.54 (0.30), residues: 360 loop : -0.72 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 208 HIS 0.010 0.001 HIS D 161 PHE 0.028 0.002 PHE C 21 TYR 0.016 0.001 TYR E 77 ARG 0.002 0.000 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 960) hydrogen bonds : angle 4.97947 ( 2588) metal coordination : bond 0.01046 ( 32) metal coordination : angle 2.06288 ( 14) covalent geometry : bond 0.00486 (19826) covalent geometry : angle 0.58704 (27584) *********************** 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 240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8398 (mmm) cc_final: 0.8167 (mmm) REVERT: B 3 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7154 (mm-30) REVERT: B 12 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: B 220 MET cc_start: 0.7987 (mmm) cc_final: 0.7552 (mmm) REVERT: C 62 TRP cc_start: 0.7260 (m-10) cc_final: 0.6999 (m-10) REVERT: C 64 MET cc_start: 0.7704 (ttp) cc_final: 0.7389 (ttp) REVERT: C 85 TYR cc_start: 0.7534 (t80) cc_final: 0.6964 (t80) REVERT: C 169 ASN cc_start: 0.6644 (m-40) cc_final: 0.5933 (t0) REVERT: C 196 MET cc_start: 0.7850 (ptt) cc_final: 0.7551 (ptt) REVERT: C 205 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8617 (mt-10) REVERT: D 134 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: D 195 ASN cc_start: 0.8839 (m-40) cc_final: 0.7691 (m110) REVERT: D 205 GLU cc_start: 0.8391 (mp0) cc_final: 0.7479 (mp0) REVERT: D 220 MET cc_start: 0.8757 (mmm) cc_final: 0.8004 (mmm) REVERT: D 251 GLU cc_start: 0.7430 (tp30) cc_final: 0.7142 (tp30) REVERT: D 269 GLU cc_start: 0.6152 (pt0) cc_final: 0.5864 (pt0) REVERT: E 218 MET cc_start: 0.8403 (mmm) cc_final: 0.8175 (mmm) REVERT: F 3 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7172 (mm-30) REVERT: F 12 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.7061 (m-70) REVERT: F 220 MET cc_start: 0.7983 (mmm) cc_final: 0.7559 (mmm) REVERT: G 62 TRP cc_start: 0.7260 (m-10) cc_final: 0.7005 (m-10) REVERT: G 64 MET cc_start: 0.7710 (ttp) cc_final: 0.7388 (ttp) REVERT: G 85 TYR cc_start: 0.7536 (t80) cc_final: 0.6963 (t80) REVERT: G 169 ASN cc_start: 0.6643 (m-40) cc_final: 0.5931 (t0) REVERT: G 196 MET cc_start: 0.7848 (ptt) cc_final: 0.7553 (ptt) REVERT: G 205 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8614 (mt-10) REVERT: H 134 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: H 205 GLU cc_start: 0.8390 (mp0) cc_final: 0.7505 (mp0) REVERT: H 220 MET cc_start: 0.8759 (mmm) cc_final: 0.8000 (mmm) REVERT: H 251 GLU cc_start: 0.7426 (tp30) cc_final: 0.7139 (tp30) REVERT: H 269 GLU cc_start: 0.6162 (pt0) cc_final: 0.5873 (pt0) outliers start: 31 outliers final: 24 residues processed: 228 average time/residue: 0.3125 time to fit residues: 108.2421 Evaluate side-chains 230 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095051 restraints weight = 39468.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093575 restraints weight = 23494.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094255 restraints weight = 18249.284| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19858 Z= 0.204 Angle : 0.588 7.790 27598 Z= 0.320 Chirality : 0.040 0.136 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.196 87.096 3740 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.05 % Allowed : 15.98 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1936 helix: 1.48 (0.18), residues: 822 sheet: 0.43 (0.29), residues: 366 loop : -0.70 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 208 HIS 0.006 0.001 HIS A 9 PHE 0.020 0.001 PHE C 21 TYR 0.015 0.001 TYR E 77 ARG 0.004 0.000 ARG H 20 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 960) hydrogen bonds : angle 4.89942 ( 2588) metal coordination : bond 0.00992 ( 32) metal coordination : angle 2.19899 ( 14) covalent geometry : bond 0.00465 (19826) covalent geometry : angle 0.58622 (27584) *********************** 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 245 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8418 (mmm) cc_final: 0.8177 (mmm) REVERT: C 62 TRP cc_start: 0.7274 (m-10) cc_final: 0.7003 (m-10) REVERT: C 64 MET cc_start: 0.7856 (ttp) cc_final: 0.7545 (ttm) REVERT: C 85 TYR cc_start: 0.7759 (t80) cc_final: 0.7268 (t80) REVERT: C 169 ASN cc_start: 0.6525 (m-40) cc_final: 0.5924 (t0) REVERT: C 205 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8592 (mt-10) REVERT: D 134 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: D 195 ASN cc_start: 0.8889 (m-40) cc_final: 0.8256 (m110) REVERT: D 205 GLU cc_start: 0.8408 (mp0) cc_final: 0.7625 (mp0) REVERT: D 220 MET cc_start: 0.8747 (mmm) cc_final: 0.7985 (mmm) REVERT: D 269 GLU cc_start: 0.6277 (pt0) cc_final: 0.5985 (pt0) REVERT: E 218 MET cc_start: 0.8418 (mmm) cc_final: 0.8183 (mmm) REVERT: G 62 TRP cc_start: 0.7269 (m-10) cc_final: 0.7002 (m-10) REVERT: G 64 MET cc_start: 0.7859 (ttp) cc_final: 0.7542 (ttm) REVERT: G 85 TYR cc_start: 0.7759 (t80) cc_final: 0.7268 (t80) REVERT: G 169 ASN cc_start: 0.6527 (m-40) cc_final: 0.5924 (t0) REVERT: G 205 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8589 (mt-10) REVERT: H 15 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7057 (p0) REVERT: H 134 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: H 196 MET cc_start: 0.6575 (mmt) cc_final: 0.5755 (mmm) REVERT: H 205 GLU cc_start: 0.8376 (mp0) cc_final: 0.7439 (mp0) REVERT: H 220 MET cc_start: 0.8784 (mmm) cc_final: 0.8033 (mmm) REVERT: H 269 GLU cc_start: 0.6264 (pt0) cc_final: 0.5971 (pt0) outliers start: 34 outliers final: 24 residues processed: 234 average time/residue: 0.3130 time to fit residues: 111.8941 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 113 MET 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 41 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096161 restraints weight = 39364.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094228 restraints weight = 23060.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094991 restraints weight = 18522.254| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3189 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= 0.182 Angle : 0.576 7.537 27598 Z= 0.313 Chirality : 0.039 0.137 3002 Planarity : 0.004 0.036 3000 Dihedral : 22.184 86.209 3740 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.87 % Allowed : 16.71 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1936 helix: 1.54 (0.19), residues: 820 sheet: 0.48 (0.29), residues: 366 loop : -0.72 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 208 HIS 0.005 0.001 HIS A 9 PHE 0.017 0.001 PHE G 21 TYR 0.014 0.001 TYR E 77 ARG 0.005 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 960) hydrogen bonds : angle 4.83011 ( 2588) metal coordination : bond 0.00843 ( 32) metal coordination : angle 2.14229 ( 14) covalent geometry : bond 0.00415 (19826) covalent geometry : angle 0.57388 (27584) *********************** 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 228 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8409 (mmm) cc_final: 0.8187 (mmm) REVERT: B 220 MET cc_start: 0.7953 (mmm) cc_final: 0.7637 (mmm) REVERT: C 64 MET cc_start: 0.7936 (ttp) cc_final: 0.7719 (ttm) REVERT: C 85 TYR cc_start: 0.7632 (t80) cc_final: 0.7369 (t80) REVERT: C 169 ASN cc_start: 0.6252 (m-40) cc_final: 0.5703 (t0) REVERT: C 205 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8536 (mt-10) REVERT: D 134 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: D 195 ASN cc_start: 0.8831 (m-40) cc_final: 0.8223 (m110) REVERT: D 205 GLU cc_start: 0.8396 (mp0) cc_final: 0.7571 (mp0) REVERT: D 220 MET cc_start: 0.8715 (mmm) cc_final: 0.8027 (mmm) REVERT: D 266 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 269 GLU cc_start: 0.6279 (pt0) cc_final: 0.5970 (pt0) REVERT: E 218 MET cc_start: 0.8403 (mmm) cc_final: 0.8188 (mmm) REVERT: F 220 MET cc_start: 0.7946 (mmm) cc_final: 0.7638 (mmm) REVERT: G 64 MET cc_start: 0.7939 (ttp) cc_final: 0.7718 (ttm) REVERT: G 85 TYR cc_start: 0.7630 (t80) cc_final: 0.7370 (t80) REVERT: G 169 ASN cc_start: 0.6246 (m-40) cc_final: 0.5697 (t0) REVERT: G 205 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8530 (mt-10) REVERT: H 15 ASN cc_start: 0.7777 (m-40) cc_final: 0.7099 (p0) REVERT: H 134 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: H 195 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7788 (m-40) REVERT: H 196 MET cc_start: 0.6592 (mmt) cc_final: 0.5789 (mmm) REVERT: H 205 GLU cc_start: 0.8399 (mp0) cc_final: 0.7577 (mp0) REVERT: H 220 MET cc_start: 0.8715 (mmm) cc_final: 0.8026 (mmm) REVERT: H 266 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7580 (tm-30) REVERT: H 269 GLU cc_start: 0.6256 (pt0) cc_final: 0.5954 (pt0) outliers start: 31 outliers final: 25 residues processed: 220 average time/residue: 0.3370 time to fit residues: 114.6469 Evaluate side-chains 213 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 123 ASN H 79 HIS ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.132955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097665 restraints weight = 39310.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096642 restraints weight = 20376.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097576 restraints weight = 14862.683| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19858 Z= 0.130 Angle : 0.557 8.076 27598 Z= 0.301 Chirality : 0.038 0.131 3002 Planarity : 0.004 0.037 3000 Dihedral : 21.958 82.214 3740 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.75 % Allowed : 17.55 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1936 helix: 1.62 (0.19), residues: 820 sheet: 0.32 (0.28), residues: 384 loop : -0.62 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 208 HIS 0.011 0.001 HIS D 161 PHE 0.018 0.001 PHE C 21 TYR 0.011 0.001 TYR B 177 ARG 0.006 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 960) hydrogen bonds : angle 4.68174 ( 2588) metal coordination : bond 0.00945 ( 32) metal coordination : angle 2.72333 ( 14) covalent geometry : bond 0.00295 (19826) covalent geometry : angle 0.55328 (27584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 149 TYR cc_start: 0.6095 (t80) cc_final: 0.5853 (m-80) REVERT: B 220 MET cc_start: 0.8061 (mmm) cc_final: 0.7626 (mmm) REVERT: C 64 MET cc_start: 0.7882 (ttp) cc_final: 0.7392 (ttm) REVERT: C 85 TYR cc_start: 0.7565 (t80) cc_final: 0.7324 (t80) REVERT: C 158 GLU cc_start: 0.7937 (tp30) cc_final: 0.7543 (tp30) REVERT: C 169 ASN cc_start: 0.6196 (m-40) cc_final: 0.5601 (t0) REVERT: C 205 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8580 (mt-10) REVERT: D 134 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: D 195 ASN cc_start: 0.8894 (m-40) cc_final: 0.8265 (m110) REVERT: D 205 GLU cc_start: 0.8378 (mp0) cc_final: 0.7558 (mp0) REVERT: D 220 MET cc_start: 0.8728 (mmm) cc_final: 0.7959 (mmm) REVERT: D 266 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 269 GLU cc_start: 0.6214 (pt0) cc_final: 0.5927 (pt0) REVERT: F 3 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7086 (mm-30) REVERT: F 149 TYR cc_start: 0.6060 (t80) cc_final: 0.5827 (m-80) REVERT: F 220 MET cc_start: 0.8055 (mmm) cc_final: 0.7627 (mmm) REVERT: G 64 MET cc_start: 0.7868 (ttp) cc_final: 0.7372 (ttm) REVERT: G 85 TYR cc_start: 0.7569 (t80) cc_final: 0.7329 (t80) REVERT: G 158 GLU cc_start: 0.7918 (tp30) cc_final: 0.7524 (tp30) REVERT: G 169 ASN cc_start: 0.6201 (m-40) cc_final: 0.5604 (t0) REVERT: G 205 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8575 (mt-10) REVERT: H 15 ASN cc_start: 0.7610 (m-40) cc_final: 0.7140 (p0) REVERT: H 134 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: H 205 GLU cc_start: 0.8374 (mp0) cc_final: 0.7551 (mp0) REVERT: H 220 MET cc_start: 0.8737 (mmm) cc_final: 0.7960 (mmm) REVERT: H 266 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7581 (tm-30) REVERT: H 269 GLU cc_start: 0.6194 (pt0) cc_final: 0.5906 (pt0) outliers start: 29 outliers final: 20 residues processed: 231 average time/residue: 0.2968 time to fit residues: 105.8537 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE 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 182 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093339 restraints weight = 39617.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091595 restraints weight = 24898.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092422 restraints weight = 18625.528| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19858 Z= 0.253 Angle : 0.641 8.239 27598 Z= 0.346 Chirality : 0.042 0.144 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.391 87.598 3740 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.51 % Allowed : 17.85 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1936 helix: 1.43 (0.19), residues: 818 sheet: 0.52 (0.30), residues: 340 loop : -0.75 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 208 HIS 0.009 0.001 HIS A 161 PHE 0.016 0.002 PHE B 88 TYR 0.017 0.002 TYR E 77 ARG 0.006 0.001 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 960) hydrogen bonds : angle 4.88435 ( 2588) metal coordination : bond 0.01427 ( 32) metal coordination : angle 2.74927 ( 14) covalent geometry : bond 0.00577 (19826) covalent geometry : angle 0.63787 (27584) ********************** 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 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.8009 (mmm) cc_final: 0.7638 (mmm) REVERT: C 158 GLU cc_start: 0.7812 (tp30) cc_final: 0.7427 (tp30) REVERT: C 169 ASN cc_start: 0.6222 (m-40) cc_final: 0.5704 (t0) REVERT: C 205 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8520 (mt-10) REVERT: D 134 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: D 143 HIS cc_start: 0.8574 (t70) cc_final: 0.8133 (t-90) REVERT: D 205 GLU cc_start: 0.8424 (mp0) cc_final: 0.7621 (mp0) REVERT: D 220 MET cc_start: 0.8695 (mmm) cc_final: 0.7974 (mmm) REVERT: D 266 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7639 (tm-30) REVERT: D 269 GLU cc_start: 0.5979 (pt0) cc_final: 0.5699 (pt0) REVERT: F 220 MET cc_start: 0.8008 (mmm) cc_final: 0.7643 (mmm) REVERT: G 158 GLU cc_start: 0.7803 (tp30) cc_final: 0.7418 (tp30) REVERT: G 169 ASN cc_start: 0.6214 (m-40) cc_final: 0.5698 (t0) REVERT: G 205 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8514 (mt-10) REVERT: H 15 ASN cc_start: 0.7831 (m-40) cc_final: 0.7207 (p0) REVERT: H 134 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: H 143 HIS cc_start: 0.8575 (t70) cc_final: 0.8129 (t-90) REVERT: H 195 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7701 (m-40) REVERT: H 205 GLU cc_start: 0.8420 (mp0) cc_final: 0.7592 (mp0) REVERT: H 220 MET cc_start: 0.8693 (mmm) cc_final: 0.7972 (mmm) REVERT: H 266 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7646 (tm-30) REVERT: H 269 GLU cc_start: 0.5876 (pt0) cc_final: 0.5593 (pt0) outliers start: 25 outliers final: 18 residues processed: 214 average time/residue: 0.2976 time to fit residues: 97.6865 Evaluate side-chains 207 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 195 ASN 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 121 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.132423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096545 restraints weight = 39287.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096421 restraints weight = 19244.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097157 restraints weight = 14484.059| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19858 Z= 0.135 Angle : 0.574 8.473 27598 Z= 0.310 Chirality : 0.039 0.176 3002 Planarity : 0.004 0.038 3000 Dihedral : 22.002 82.562 3740 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.39 % Allowed : 18.34 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1936 helix: 1.56 (0.19), residues: 820 sheet: 0.34 (0.29), residues: 372 loop : -0.57 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 208 HIS 0.007 0.001 HIS A 161 PHE 0.017 0.001 PHE C 21 TYR 0.011 0.001 TYR G 77 ARG 0.010 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 960) hydrogen bonds : angle 4.69424 ( 2588) metal coordination : bond 0.00891 ( 32) metal coordination : angle 2.38458 ( 14) covalent geometry : bond 0.00306 (19826) covalent geometry : angle 0.57145 (27584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.23 seconds wall clock time: 102 minutes 50.91 seconds (6170.91 seconds total)