Starting phenix.real_space_refine on Sat Sep 28 09:33:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_26737.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_26737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_26737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_26737.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/09_2024/7usf_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.07, per 1000 atoms: 0.64 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: 5.19 Conformation dependent library (CDL) restraints added in 1.9 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: 8.82 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: 7.81 Time building geometry restraints manager: 5.48 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'B' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 177 throu \ gh 264)) selection = (chain 'D' and (resid 2 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 264)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'F' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 177 throu \ gh 264)) selection = (chain 'H' and (resid 2 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 264)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 54.090 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.540 ------------------------------------------------------------------------------- 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 0.031 19826 Z= 0.183 Angle : 0.553 10.252 27584 Z= 0.318 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 1.962 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: 0.3069 time to fit residues: 147.1910 Evaluate side-chains 208 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 19826 Z= 0.423 Angle : 0.641 7.594 27584 Z= 0.353 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 *********************** 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 fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 2.231 Fit side-chains REVERT: A 134 GLU cc_start: 0.8248 (tp30) cc_final: 0.7975 (tp30) REVERT: B 3 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 7 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7473 (mt-10) REVERT: B 130 ARG cc_start: 0.7929 (mmp-170) cc_final: 0.7648 (mmp80) REVERT: B 134 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 201 HIS cc_start: 0.8291 (m-70) cc_final: 0.8043 (m-70) REVERT: B 220 MET cc_start: 0.7982 (tpt) cc_final: 0.7605 (mmm) REVERT: C 65 ASP cc_start: 0.8813 (t70) cc_final: 0.8399 (t0) REVERT: C 85 TYR cc_start: 0.7394 (t80) cc_final: 0.7126 (t80) REVERT: C 127 TYR cc_start: 0.6830 (m-10) cc_final: 0.6623 (m-10) REVERT: C 205 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8714 (mt-10) REVERT: D 7 GLU cc_start: 0.8902 (pt0) cc_final: 0.8465 (pm20) REVERT: D 20 ARG cc_start: 0.8518 (ptm-80) cc_final: 0.8316 (ptm-80) REVERT: D 65 ASP cc_start: 0.8448 (t0) cc_final: 0.8194 (t70) REVERT: D 134 GLU cc_start: 0.8490 (mp0) cc_final: 0.8124 (tm-30) REVERT: D 161 HIS cc_start: 0.7295 (m-70) cc_final: 0.6463 (m90) REVERT: D 195 ASN cc_start: 0.8951 (m-40) cc_final: 0.8619 (t0) REVERT: D 196 MET cc_start: 0.7498 (mmm) cc_final: 0.6660 (mmm) REVERT: D 205 GLU cc_start: 0.8239 (mp0) cc_final: 0.7169 (mp0) REVERT: D 220 MET cc_start: 0.8953 (mmm) cc_final: 0.8158 (mmm) REVERT: D 223 ASP cc_start: 0.8651 (t70) cc_final: 0.7881 (t0) REVERT: D 251 GLU cc_start: 0.8003 (tp30) cc_final: 0.7760 (tp30) REVERT: D 265 THR cc_start: 0.8534 (m) cc_final: 0.8089 (p) REVERT: E 64 MET cc_start: 0.9064 (ttm) cc_final: 0.8809 (ttm) REVERT: E 134 GLU cc_start: 0.8249 (tp30) cc_final: 0.7972 (tp30) REVERT: F 3 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7481 (mm-30) REVERT: F 7 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7475 (mt-10) REVERT: F 130 ARG cc_start: 0.7927 (mmp-170) cc_final: 0.7647 (mmp80) REVERT: F 134 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8021 (tm-30) REVERT: F 201 HIS cc_start: 0.8295 (m-70) cc_final: 0.8048 (m-70) REVERT: F 220 MET cc_start: 0.7983 (tpt) cc_final: 0.7612 (mmm) REVERT: G 65 ASP cc_start: 0.8814 (t70) cc_final: 0.8398 (t0) REVERT: G 85 TYR cc_start: 0.7397 (t80) cc_final: 0.7124 (t80) REVERT: G 127 TYR cc_start: 0.6834 (m-10) cc_final: 0.6621 (m-10) REVERT: G 205 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8717 (mt-10) REVERT: H 7 GLU cc_start: 0.8901 (pt0) cc_final: 0.8462 (pm20) REVERT: H 20 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.8314 (ptm-80) REVERT: H 65 ASP cc_start: 0.8453 (t0) cc_final: 0.8200 (t70) REVERT: H 134 GLU cc_start: 0.8490 (mp0) cc_final: 0.8126 (tm-30) REVERT: H 161 HIS cc_start: 0.7292 (m-70) cc_final: 0.6459 (m90) REVERT: H 195 ASN cc_start: 0.8953 (m-40) cc_final: 0.8618 (t0) REVERT: H 196 MET cc_start: 0.7497 (mmm) cc_final: 0.6654 (mmm) REVERT: H 205 GLU cc_start: 0.8240 (mp0) cc_final: 0.7169 (mp0) REVERT: H 220 MET cc_start: 0.8955 (mmm) cc_final: 0.8158 (mmm) REVERT: H 223 ASP cc_start: 0.8651 (t70) cc_final: 0.7880 (t0) REVERT: H 251 GLU cc_start: 0.8002 (tp30) cc_final: 0.7758 (tp30) REVERT: H 265 THR cc_start: 0.8534 (m) cc_final: 0.8088 (p) outliers start: 24 outliers final: 14 residues processed: 260 average time/residue: 0.3073 time to fit residues: 121.6901 Evaluate side-chains 224 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 105 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 0.0370 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- 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** E 117 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19826 Z= 0.483 Angle : 0.674 10.179 27584 Z= 0.368 Chirality : 0.044 0.136 3002 Planarity : 0.005 0.049 3000 Dihedral : 22.395 90.696 3740 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.20 % Allowed : 11.34 % Favored : 85.46 % 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: 0.31 (0.20), residues: 1936 helix: 1.04 (0.18), residues: 822 sheet: 0.51 (0.31), residues: 338 loop : -0.78 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 208 HIS 0.009 0.002 HIS E 9 PHE 0.019 0.002 PHE B 88 TYR 0.020 0.002 TYR C 77 ARG 0.004 0.001 ARG D 94 *********************** 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 279 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 2.138 Fit side-chains REVERT: B 130 ARG cc_start: 0.7927 (mmp-170) cc_final: 0.7659 (mmp80) REVERT: B 134 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 201 HIS cc_start: 0.8265 (m-70) cc_final: 0.7980 (m-70) REVERT: B 220 MET cc_start: 0.7961 (tpt) cc_final: 0.7229 (mmm) REVERT: C 62 TRP cc_start: 0.7194 (m-10) cc_final: 0.6334 (m-10) REVERT: C 65 ASP cc_start: 0.8792 (t0) cc_final: 0.8432 (t0) REVERT: C 85 TYR cc_start: 0.7467 (t80) cc_final: 0.7220 (t80) REVERT: C 97 GLU cc_start: 0.7604 (mp0) cc_final: 0.7280 (mp0) REVERT: C 205 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 7 GLU cc_start: 0.8904 (pt0) cc_final: 0.8437 (pm20) REVERT: D 65 ASP cc_start: 0.8397 (t0) cc_final: 0.8059 (t70) REVERT: D 134 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: D 161 HIS cc_start: 0.7468 (m-70) cc_final: 0.6872 (m90) REVERT: D 196 MET cc_start: 0.7530 (mmm) cc_final: 0.6590 (mmm) REVERT: D 205 GLU cc_start: 0.8079 (mp0) cc_final: 0.7087 (mp0) REVERT: D 220 MET cc_start: 0.8874 (mmm) cc_final: 0.7562 (mmm) REVERT: D 223 ASP cc_start: 0.8677 (t70) cc_final: 0.8050 (t0) REVERT: E 64 MET cc_start: 0.9075 (ttm) cc_final: 0.8811 (ttm) REVERT: F 130 ARG cc_start: 0.7927 (mmp-170) cc_final: 0.7657 (mmp80) REVERT: F 134 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8173 (tm-30) REVERT: F 201 HIS cc_start: 0.8271 (m-70) cc_final: 0.7984 (m-70) REVERT: F 220 MET cc_start: 0.7963 (tpt) cc_final: 0.7237 (mmm) REVERT: G 62 TRP cc_start: 0.7194 (m-10) cc_final: 0.6333 (m-10) REVERT: G 65 ASP cc_start: 0.8790 (t0) cc_final: 0.8429 (t0) REVERT: G 85 TYR cc_start: 0.7469 (t80) cc_final: 0.7217 (t80) REVERT: G 97 GLU cc_start: 0.7608 (mp0) cc_final: 0.7284 (mp0) REVERT: G 205 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8559 (mt-10) REVERT: H 7 GLU cc_start: 0.8903 (pt0) cc_final: 0.8436 (pm20) REVERT: H 65 ASP cc_start: 0.8397 (t0) cc_final: 0.8063 (t70) REVERT: H 134 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: H 161 HIS cc_start: 0.7463 (m-70) cc_final: 0.6868 (m90) REVERT: H 196 MET cc_start: 0.7535 (mmm) cc_final: 0.6593 (mmm) REVERT: H 205 GLU cc_start: 0.8079 (mp0) cc_final: 0.7086 (mp0) REVERT: H 220 MET cc_start: 0.8872 (mmm) cc_final: 0.7566 (mmm) REVERT: H 223 ASP cc_start: 0.8679 (t70) cc_final: 0.8051 (t0) outliers start: 53 outliers final: 32 residues processed: 263 average time/residue: 0.3048 time to fit residues: 122.4190 Evaluate side-chains 242 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 6.9990 chunk 143 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19826 Z= 0.311 Angle : 0.587 9.123 27584 Z= 0.321 Chirality : 0.040 0.136 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.218 88.080 3740 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.47 % Allowed : 13.63 % Favored : 83.90 % 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: 0.53 (0.20), residues: 1936 helix: 1.30 (0.18), residues: 822 sheet: 0.54 (0.30), residues: 348 loop : -0.74 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 208 HIS 0.006 0.001 HIS B 182 PHE 0.027 0.002 PHE G 21 TYR 0.018 0.002 TYR C 77 ARG 0.005 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7402 (mm-30) REVERT: B 7 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7445 (mt-10) REVERT: B 12 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5999 (m-70) REVERT: B 130 ARG cc_start: 0.8022 (mmp-170) cc_final: 0.7745 (mmp80) REVERT: B 134 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 220 MET cc_start: 0.7953 (tpt) cc_final: 0.7237 (mmm) REVERT: C 62 TRP cc_start: 0.7039 (m-10) cc_final: 0.5689 (m-10) REVERT: C 65 ASP cc_start: 0.8820 (t0) cc_final: 0.8448 (t0) REVERT: C 85 TYR cc_start: 0.7460 (t80) cc_final: 0.7243 (t80) REVERT: C 113 MET cc_start: 0.6393 (mtm) cc_final: 0.5666 (mtp) REVERT: C 169 ASN cc_start: 0.7286 (m-40) cc_final: 0.6256 (t0) REVERT: C 205 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8635 (mt-10) REVERT: D 7 GLU cc_start: 0.8899 (pt0) cc_final: 0.8434 (pm20) REVERT: D 134 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: D 161 HIS cc_start: 0.7517 (m-70) cc_final: 0.6735 (m90) REVERT: D 196 MET cc_start: 0.7401 (mmm) cc_final: 0.6424 (mmm) REVERT: D 205 GLU cc_start: 0.8138 (mp0) cc_final: 0.7384 (mp0) REVERT: D 220 MET cc_start: 0.8756 (mmm) cc_final: 0.7684 (mmm) REVERT: D 223 ASP cc_start: 0.8723 (t70) cc_final: 0.8162 (t0) REVERT: D 251 GLU cc_start: 0.7931 (tp30) cc_final: 0.7590 (tp30) REVERT: F 3 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7405 (mm-30) REVERT: F 7 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7444 (mt-10) REVERT: F 12 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5990 (m-70) REVERT: F 130 ARG cc_start: 0.8026 (mmp-170) cc_final: 0.7749 (mmp80) REVERT: F 134 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8165 (tm-30) REVERT: F 220 MET cc_start: 0.7958 (tpt) cc_final: 0.7246 (mmm) REVERT: G 62 TRP cc_start: 0.7041 (m-10) cc_final: 0.5695 (m-10) REVERT: G 65 ASP cc_start: 0.8818 (t0) cc_final: 0.8445 (t0) REVERT: G 85 TYR cc_start: 0.7463 (t80) cc_final: 0.7242 (t80) REVERT: G 113 MET cc_start: 0.6394 (mtm) cc_final: 0.5666 (mtp) REVERT: G 169 ASN cc_start: 0.7291 (m-40) cc_final: 0.6259 (t0) REVERT: G 205 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8635 (mt-10) REVERT: H 7 GLU cc_start: 0.8901 (pt0) cc_final: 0.8432 (pm20) REVERT: H 134 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: H 161 HIS cc_start: 0.7512 (m-70) cc_final: 0.6733 (m90) REVERT: H 196 MET cc_start: 0.7405 (mmm) cc_final: 0.6422 (mmm) REVERT: H 205 GLU cc_start: 0.8140 (mp0) cc_final: 0.7385 (mp0) REVERT: H 220 MET cc_start: 0.8755 (mmm) cc_final: 0.7685 (mmm) REVERT: H 223 ASP cc_start: 0.8723 (t70) cc_final: 0.8162 (t0) REVERT: H 251 GLU cc_start: 0.7938 (tp30) cc_final: 0.7594 (tp30) outliers start: 41 outliers final: 19 residues processed: 249 average time/residue: 0.3151 time to fit residues: 120.2272 Evaluate side-chains 223 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 26 THR 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 E residue 34 VAL 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 G residue 26 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 30.0000 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 117 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19826 Z= 0.369 Angle : 0.614 9.492 27584 Z= 0.334 Chirality : 0.042 0.143 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.342 88.952 3740 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.14 % Allowed : 14.48 % Favored : 82.39 % 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: 0.46 (0.20), residues: 1936 helix: 1.31 (0.18), residues: 822 sheet: 0.52 (0.31), residues: 326 loop : -0.84 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 208 HIS 0.007 0.001 HIS A 9 PHE 0.015 0.002 PHE F 88 TYR 0.011 0.002 TYR F 177 ARG 0.003 0.000 ARG H 94 *********************** 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 fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 7 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7565 (mt-10) REVERT: B 12 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.5903 (m-70) REVERT: B 130 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7739 (mmp80) REVERT: B 134 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 220 MET cc_start: 0.7972 (tpt) cc_final: 0.7254 (mmm) REVERT: C 64 MET cc_start: 0.7913 (ttp) cc_final: 0.7577 (ttm) REVERT: C 65 ASP cc_start: 0.8779 (t0) cc_final: 0.8416 (t0) REVERT: C 113 MET cc_start: 0.6774 (mtm) cc_final: 0.6496 (mtp) REVERT: C 169 ASN cc_start: 0.7191 (m-40) cc_final: 0.6168 (t0) REVERT: C 205 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8678 (mt-10) REVERT: D 7 GLU cc_start: 0.8905 (pt0) cc_final: 0.8444 (pm20) REVERT: D 134 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: D 161 HIS cc_start: 0.7442 (m-70) cc_final: 0.7165 (m170) REVERT: D 205 GLU cc_start: 0.8153 (mp0) cc_final: 0.7411 (mp0) REVERT: D 220 MET cc_start: 0.8674 (mmm) cc_final: 0.7182 (mmm) REVERT: D 223 ASP cc_start: 0.8694 (t70) cc_final: 0.8143 (t0) REVERT: F 3 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7440 (mm-30) REVERT: F 7 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7564 (mt-10) REVERT: F 12 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.5890 (m-70) REVERT: F 130 ARG cc_start: 0.8031 (mmp-170) cc_final: 0.7740 (mmp80) REVERT: F 134 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7802 (tm-30) REVERT: F 220 MET cc_start: 0.7978 (tpt) cc_final: 0.7261 (mmm) REVERT: G 64 MET cc_start: 0.7921 (ttp) cc_final: 0.7583 (ttm) REVERT: G 65 ASP cc_start: 0.8774 (t0) cc_final: 0.8410 (t0) REVERT: G 113 MET cc_start: 0.6771 (mtm) cc_final: 0.6494 (mtp) REVERT: G 169 ASN cc_start: 0.7197 (m-40) cc_final: 0.6174 (t0) REVERT: G 205 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8678 (mt-10) REVERT: H 7 GLU cc_start: 0.8904 (pt0) cc_final: 0.8442 (pm20) REVERT: H 134 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: H 161 HIS cc_start: 0.7440 (m-70) cc_final: 0.7163 (m170) REVERT: H 205 GLU cc_start: 0.8153 (mp0) cc_final: 0.7412 (mp0) REVERT: H 220 MET cc_start: 0.8670 (mmm) cc_final: 0.7188 (mmm) REVERT: H 223 ASP cc_start: 0.8692 (t70) cc_final: 0.8142 (t0) outliers start: 52 outliers final: 39 residues processed: 250 average time/residue: 0.3096 time to fit residues: 118.3004 Evaluate side-chains 235 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 A residue 208 TRP 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 202 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 132 ILE 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 25 ILE Chi-restraints excluded: chain D residue 119 ILE 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 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 208 TRP 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 F residue 254 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 132 ILE 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 25 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 117 GLN D 186 HIS E 52 ASN H 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19826 Z= 0.202 Angle : 0.545 7.511 27584 Z= 0.298 Chirality : 0.038 0.130 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.068 85.076 3740 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.65 % Allowed : 15.74 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.18), residues: 824 sheet: 0.48 (0.29), residues: 364 loop : -0.73 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 208 HIS 0.005 0.001 HIS B 105 PHE 0.011 0.001 PHE G 21 TYR 0.015 0.001 TYR G 85 ARG 0.003 0.000 ARG A 54 *********************** 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 257 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8881 (mp0) cc_final: 0.8626 (mp0) REVERT: A 218 MET cc_start: 0.8612 (mmm) cc_final: 0.8358 (mmm) REVERT: B 3 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 7 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7523 (mt-10) REVERT: B 12 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5738 (m-70) REVERT: B 130 ARG cc_start: 0.8002 (mmp-170) cc_final: 0.7701 (mmp80) REVERT: B 134 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 220 MET cc_start: 0.7997 (tpt) cc_final: 0.7297 (mmm) REVERT: C 64 MET cc_start: 0.8108 (ttp) cc_final: 0.7853 (ttm) REVERT: C 65 ASP cc_start: 0.8800 (t0) cc_final: 0.8433 (t0) REVERT: C 113 MET cc_start: 0.6465 (mtm) cc_final: 0.5918 (mtp) REVERT: C 169 ASN cc_start: 0.6842 (m-40) cc_final: 0.6058 (t0) REVERT: C 205 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8619 (mt-10) REVERT: D 7 GLU cc_start: 0.8874 (pt0) cc_final: 0.8413 (pm20) REVERT: D 15 ASN cc_start: 0.7936 (m-40) cc_final: 0.7183 (p0) REVERT: D 134 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: D 195 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: D 196 MET cc_start: 0.6476 (mmt) cc_final: 0.5911 (mmm) REVERT: D 205 GLU cc_start: 0.8139 (mp0) cc_final: 0.7341 (mp0) REVERT: D 220 MET cc_start: 0.8668 (mmm) cc_final: 0.7269 (mmm) REVERT: D 223 ASP cc_start: 0.8693 (t70) cc_final: 0.8114 (t0) REVERT: D 251 GLU cc_start: 0.7676 (tp30) cc_final: 0.7378 (tp30) REVERT: E 71 GLU cc_start: 0.8886 (mp0) cc_final: 0.8638 (mp0) REVERT: E 218 MET cc_start: 0.8608 (mmm) cc_final: 0.8359 (mmm) REVERT: F 3 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7425 (mm-30) REVERT: F 7 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7523 (mt-10) REVERT: F 12 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5738 (m-70) REVERT: F 130 ARG cc_start: 0.8002 (mmp-170) cc_final: 0.7701 (mmp80) REVERT: F 134 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8121 (tm-30) REVERT: F 220 MET cc_start: 0.7999 (tpt) cc_final: 0.7302 (mmm) REVERT: G 64 MET cc_start: 0.8111 (ttp) cc_final: 0.7857 (ttm) REVERT: G 65 ASP cc_start: 0.8799 (t0) cc_final: 0.8432 (t0) REVERT: G 113 MET cc_start: 0.6466 (mtm) cc_final: 0.5916 (mtp) REVERT: G 169 ASN cc_start: 0.6846 (m-40) cc_final: 0.6064 (t0) REVERT: G 205 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8623 (mt-10) REVERT: H 7 GLU cc_start: 0.8874 (pt0) cc_final: 0.8411 (pm20) REVERT: H 15 ASN cc_start: 0.7930 (m-40) cc_final: 0.7179 (p0) REVERT: H 134 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: H 195 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: H 196 MET cc_start: 0.6476 (mmt) cc_final: 0.5912 (mmm) REVERT: H 205 GLU cc_start: 0.8141 (mp0) cc_final: 0.7343 (mp0) REVERT: H 220 MET cc_start: 0.8663 (mmm) cc_final: 0.7266 (mmm) REVERT: H 223 ASP cc_start: 0.8695 (t70) cc_final: 0.8116 (t0) REVERT: H 251 GLU cc_start: 0.7685 (tp30) cc_final: 0.7384 (tp30) outliers start: 44 outliers final: 27 residues processed: 245 average time/residue: 0.3279 time to fit residues: 123.9566 Evaluate side-chains 236 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 208 TRP 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 164 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 ASN 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 129 SER Chi-restraints excluded: chain E residue 208 TRP 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 164 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 202 optimal weight: 0.0020 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19826 Z= 0.193 Angle : 0.531 7.078 27584 Z= 0.292 Chirality : 0.038 0.131 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.043 83.639 3740 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 16.41 % Favored : 81.18 % 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: 0.77 (0.20), residues: 1936 helix: 1.64 (0.18), residues: 824 sheet: 0.43 (0.28), residues: 378 loop : -0.71 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 208 HIS 0.005 0.001 HIS G 9 PHE 0.010 0.001 PHE G 23 TYR 0.012 0.001 TYR G 85 ARG 0.003 0.000 ARG D 159 *********************** 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 264 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8871 (mp0) cc_final: 0.8602 (mp0) REVERT: A 218 MET cc_start: 0.8620 (mmm) cc_final: 0.8375 (mmm) REVERT: B 3 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 7 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7465 (mt-10) REVERT: B 12 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.5696 (m-70) REVERT: B 130 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7687 (mmp80) REVERT: B 134 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8105 (tm-30) REVERT: B 220 MET cc_start: 0.7974 (tpt) cc_final: 0.7298 (mmm) REVERT: C 65 ASP cc_start: 0.8820 (t0) cc_final: 0.8468 (t0) REVERT: C 113 MET cc_start: 0.6590 (mtm) cc_final: 0.6152 (mtp) REVERT: C 169 ASN cc_start: 0.6566 (m-40) cc_final: 0.5776 (t0) REVERT: C 192 ASN cc_start: 0.6218 (m-40) cc_final: 0.5982 (m-40) REVERT: C 205 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8596 (mt-10) REVERT: D 7 GLU cc_start: 0.8840 (pt0) cc_final: 0.8353 (pm20) REVERT: D 15 ASN cc_start: 0.7936 (m-40) cc_final: 0.7159 (p0) REVERT: D 134 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: D 195 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.6911 (m110) REVERT: D 196 MET cc_start: 0.6441 (mmt) cc_final: 0.5809 (mmm) REVERT: D 205 GLU cc_start: 0.8121 (mp0) cc_final: 0.7304 (mp0) REVERT: D 220 MET cc_start: 0.8612 (mmm) cc_final: 0.7253 (mmm) REVERT: D 223 ASP cc_start: 0.8695 (t70) cc_final: 0.8099 (t0) REVERT: D 251 GLU cc_start: 0.7545 (tp30) cc_final: 0.7297 (tp30) REVERT: E 71 GLU cc_start: 0.8870 (mp0) cc_final: 0.8608 (mp0) REVERT: E 218 MET cc_start: 0.8619 (mmm) cc_final: 0.8376 (mmm) REVERT: F 3 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7551 (mm-30) REVERT: F 7 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7465 (mt-10) REVERT: F 12 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5704 (m-70) REVERT: F 130 ARG cc_start: 0.7984 (mmp-170) cc_final: 0.7682 (mmp80) REVERT: F 134 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8106 (tm-30) REVERT: F 220 MET cc_start: 0.7976 (tpt) cc_final: 0.7306 (mmm) REVERT: G 65 ASP cc_start: 0.8816 (t0) cc_final: 0.8463 (t0) REVERT: G 113 MET cc_start: 0.6588 (mtm) cc_final: 0.6152 (mtp) REVERT: G 169 ASN cc_start: 0.6568 (m-40) cc_final: 0.5781 (t0) REVERT: G 192 ASN cc_start: 0.6215 (m-40) cc_final: 0.5979 (m-40) REVERT: G 205 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8600 (mt-10) REVERT: H 7 GLU cc_start: 0.8841 (pt0) cc_final: 0.8352 (pm20) REVERT: H 15 ASN cc_start: 0.7932 (m-40) cc_final: 0.7155 (p0) REVERT: H 134 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: H 195 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.6910 (m110) REVERT: H 196 MET cc_start: 0.6437 (mmt) cc_final: 0.5805 (mmm) REVERT: H 205 GLU cc_start: 0.8124 (mp0) cc_final: 0.7304 (mp0) REVERT: H 220 MET cc_start: 0.8611 (mmm) cc_final: 0.7252 (mmm) REVERT: H 223 ASP cc_start: 0.8692 (t70) cc_final: 0.8098 (t0) REVERT: H 251 GLU cc_start: 0.7553 (tp30) cc_final: 0.7304 (tp30) REVERT: H 266 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7496 (tm-30) outliers start: 40 outliers final: 25 residues processed: 252 average time/residue: 0.3134 time to fit residues: 120.1043 Evaluate side-chains 239 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 208 TRP 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 164 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 ASN 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 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 164 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 195 ASN 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 125 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN E 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19826 Z= 0.301 Angle : 0.575 7.920 27584 Z= 0.316 Chirality : 0.040 0.141 3002 Planarity : 0.004 0.035 3000 Dihedral : 22.250 86.939 3740 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.35 % Allowed : 17.13 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.18), residues: 822 sheet: 0.58 (0.29), residues: 350 loop : -0.79 (0.23), residues: 764 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 0.029 0.001 PHE G 21 TYR 0.014 0.002 TYR E 77 ARG 0.005 0.000 ARG H 159 *********************** 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 248 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 209 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8877 (mp0) cc_final: 0.8611 (mp0) REVERT: A 218 MET cc_start: 0.8622 (mmm) cc_final: 0.8350 (mmm) REVERT: A 258 ASP cc_start: 0.8276 (m-30) cc_final: 0.7840 (m-30) REVERT: B 12 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.5884 (m-70) REVERT: B 130 ARG cc_start: 0.7994 (mmp-170) cc_final: 0.7685 (mmp80) REVERT: B 134 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 220 MET cc_start: 0.8003 (tpt) cc_final: 0.7304 (mmm) REVERT: C 65 ASP cc_start: 0.8649 (t0) cc_final: 0.8356 (t0) REVERT: C 113 MET cc_start: 0.6717 (mtm) cc_final: 0.6255 (mtp) REVERT: C 158 GLU cc_start: 0.8127 (tp30) cc_final: 0.7749 (tp30) REVERT: C 169 ASN cc_start: 0.6696 (m-40) cc_final: 0.5911 (t0) REVERT: C 192 ASN cc_start: 0.6216 (m-40) cc_final: 0.5972 (m-40) REVERT: C 205 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8572 (mt-10) REVERT: D 7 GLU cc_start: 0.8846 (pt0) cc_final: 0.8433 (pm20) REVERT: D 15 ASN cc_start: 0.7967 (m-40) cc_final: 0.7007 (p0) REVERT: D 134 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: D 195 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.6826 (m110) REVERT: D 196 MET cc_start: 0.6687 (mmt) cc_final: 0.6050 (mmm) REVERT: D 205 GLU cc_start: 0.8202 (mp0) cc_final: 0.7450 (mp0) REVERT: D 220 MET cc_start: 0.8573 (mmm) cc_final: 0.7208 (mmm) REVERT: D 223 ASP cc_start: 0.8656 (t70) cc_final: 0.8046 (t0) REVERT: D 251 GLU cc_start: 0.7598 (tp30) cc_final: 0.7353 (tp30) REVERT: D 266 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 71 GLU cc_start: 0.8871 (mp0) cc_final: 0.8603 (mp0) REVERT: E 218 MET cc_start: 0.8622 (mmm) cc_final: 0.8352 (mmm) REVERT: E 258 ASP cc_start: 0.8290 (m-30) cc_final: 0.7846 (m-30) REVERT: F 12 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.5878 (m-70) REVERT: F 130 ARG cc_start: 0.7996 (mmp-170) cc_final: 0.7684 (mmp80) REVERT: F 134 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7786 (tm-30) REVERT: F 220 MET cc_start: 0.8004 (tpt) cc_final: 0.7313 (mmm) REVERT: G 65 ASP cc_start: 0.8646 (t0) cc_final: 0.8352 (t0) REVERT: G 113 MET cc_start: 0.6712 (mtm) cc_final: 0.6254 (mtp) REVERT: G 158 GLU cc_start: 0.8124 (tp30) cc_final: 0.7749 (tp30) REVERT: G 169 ASN cc_start: 0.6698 (m-40) cc_final: 0.5914 (t0) REVERT: G 192 ASN cc_start: 0.6214 (m-40) cc_final: 0.5970 (m-40) REVERT: G 205 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8576 (mt-10) REVERT: H 7 GLU cc_start: 0.8844 (pt0) cc_final: 0.8431 (pm20) REVERT: H 15 ASN cc_start: 0.7963 (m-40) cc_final: 0.7003 (p0) REVERT: H 134 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: H 195 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.6823 (m110) REVERT: H 196 MET cc_start: 0.6681 (mmt) cc_final: 0.6042 (mmm) REVERT: H 205 GLU cc_start: 0.8199 (mp0) cc_final: 0.7447 (mp0) REVERT: H 220 MET cc_start: 0.8572 (mmm) cc_final: 0.7210 (mmm) REVERT: H 223 ASP cc_start: 0.8651 (t70) cc_final: 0.8044 (t0) REVERT: H 251 GLU cc_start: 0.7599 (tp30) cc_final: 0.7353 (tp30) REVERT: H 266 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 39 outliers final: 25 residues processed: 237 average time/residue: 0.3065 time to fit residues: 111.9838 Evaluate side-chains 229 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 195 ASN 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 129 SER Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 234 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 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 193 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 0.0030 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 0.0970 chunk 187 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN C 63 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19826 Z= 0.208 Angle : 0.558 7.752 27584 Z= 0.304 Chirality : 0.038 0.134 3002 Planarity : 0.004 0.036 3000 Dihedral : 22.075 84.492 3740 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 17.79 % Favored : 79.98 % 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: 0.77 (0.20), residues: 1936 helix: 1.65 (0.19), residues: 824 sheet: 0.37 (0.28), residues: 378 loop : -0.68 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 208 HIS 0.007 0.001 HIS H 161 PHE 0.028 0.001 PHE G 21 TYR 0.012 0.001 TYR G 85 ARG 0.006 0.000 ARG E 130 *********************** 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 244 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8830 (mp0) cc_final: 0.8539 (mp0) REVERT: A 218 MET cc_start: 0.8614 (mmm) cc_final: 0.8348 (mmm) REVERT: A 258 ASP cc_start: 0.8295 (m-30) cc_final: 0.7875 (m-30) REVERT: B 3 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7137 (mm-30) REVERT: B 7 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7492 (mt-10) REVERT: B 12 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5702 (m-70) REVERT: B 130 ARG cc_start: 0.7989 (mmp-170) cc_final: 0.7680 (mmp80) REVERT: B 134 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 220 MET cc_start: 0.7986 (tpt) cc_final: 0.7310 (mmm) REVERT: C 65 ASP cc_start: 0.8608 (t0) cc_final: 0.8339 (t0) REVERT: C 113 MET cc_start: 0.6706 (mtm) cc_final: 0.6231 (mtp) REVERT: C 169 ASN cc_start: 0.6652 (m-40) cc_final: 0.5901 (t0) REVERT: C 192 ASN cc_start: 0.6082 (m-40) cc_final: 0.5855 (m-40) REVERT: C 205 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8544 (mt-10) REVERT: D 7 GLU cc_start: 0.8826 (pt0) cc_final: 0.8416 (pm20) REVERT: D 15 ASN cc_start: 0.7917 (m-40) cc_final: 0.7158 (p0) REVERT: D 134 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: D 195 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7695 (m-40) REVERT: D 205 GLU cc_start: 0.8137 (mp0) cc_final: 0.7346 (mp0) REVERT: D 220 MET cc_start: 0.8593 (mmm) cc_final: 0.7223 (mmm) REVERT: D 223 ASP cc_start: 0.8693 (t70) cc_final: 0.8100 (t0) REVERT: D 251 GLU cc_start: 0.7575 (tp30) cc_final: 0.7348 (tp30) REVERT: D 266 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 71 GLU cc_start: 0.8865 (mp0) cc_final: 0.8592 (mp0) REVERT: E 218 MET cc_start: 0.8615 (mmm) cc_final: 0.8349 (mmm) REVERT: E 258 ASP cc_start: 0.8309 (m-30) cc_final: 0.7886 (m-30) REVERT: F 3 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7141 (mm-30) REVERT: F 7 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7495 (mt-10) REVERT: F 12 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5699 (m-70) REVERT: F 130 ARG cc_start: 0.7991 (mmp-170) cc_final: 0.7681 (mmp80) REVERT: F 134 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8126 (tm-30) REVERT: F 220 MET cc_start: 0.7991 (tpt) cc_final: 0.7316 (mmm) REVERT: G 65 ASP cc_start: 0.8603 (t0) cc_final: 0.8333 (t0) REVERT: G 113 MET cc_start: 0.6701 (mtm) cc_final: 0.6226 (mtp) REVERT: G 169 ASN cc_start: 0.6648 (m-40) cc_final: 0.5897 (t0) REVERT: G 192 ASN cc_start: 0.6080 (m-40) cc_final: 0.5857 (m-40) REVERT: G 205 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8546 (mt-10) REVERT: H 7 GLU cc_start: 0.8825 (pt0) cc_final: 0.8414 (pm20) REVERT: H 15 ASN cc_start: 0.7913 (m-40) cc_final: 0.7154 (p0) REVERT: H 134 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: H 195 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7694 (m-40) REVERT: H 205 GLU cc_start: 0.8137 (mp0) cc_final: 0.7346 (mp0) REVERT: H 220 MET cc_start: 0.8591 (mmm) cc_final: 0.7222 (mmm) REVERT: H 223 ASP cc_start: 0.8687 (t70) cc_final: 0.8096 (t0) REVERT: H 251 GLU cc_start: 0.7577 (tp30) cc_final: 0.7353 (tp30) REVERT: H 266 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7580 (tm-30) outliers start: 37 outliers final: 26 residues processed: 234 average time/residue: 0.3031 time to fit residues: 108.9576 Evaluate side-chains 232 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 208 TRP 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 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 208 TRP 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 164 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 225 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 0.0570 chunk 128 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 123 ASN D 79 HIS E 52 ASN E 123 ASN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19826 Z= 0.179 Angle : 0.551 8.228 27584 Z= 0.300 Chirality : 0.038 0.287 3002 Planarity : 0.004 0.039 3000 Dihedral : 21.908 80.929 3740 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.17 % Allowed : 17.97 % Favored : 79.86 % 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: 0.88 (0.20), residues: 1936 helix: 1.77 (0.19), residues: 824 sheet: 0.37 (0.29), residues: 360 loop : -0.59 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 208 HIS 0.006 0.001 HIS H 161 PHE 0.027 0.001 PHE C 21 TYR 0.012 0.001 TYR C 85 ARG 0.007 0.000 ARG E 130 ********************** 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 253 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8869 (mp0) cc_final: 0.8582 (mp0) REVERT: A 237 THR cc_start: 0.9275 (t) cc_final: 0.8895 (p) REVERT: A 258 ASP cc_start: 0.8273 (m-30) cc_final: 0.7868 (m-30) REVERT: B 3 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 7 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7500 (mt-10) REVERT: B 11 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8327 (tt) REVERT: B 130 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7651 (mmp80) REVERT: B 134 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 149 TYR cc_start: 0.6249 (t80) cc_final: 0.5924 (m-80) REVERT: B 220 MET cc_start: 0.7993 (tpt) cc_final: 0.7352 (mmm) REVERT: C 65 ASP cc_start: 0.8525 (t0) cc_final: 0.7996 (m-30) REVERT: C 113 MET cc_start: 0.6692 (mtm) cc_final: 0.6207 (mtp) REVERT: C 205 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8519 (mt-10) REVERT: D 7 GLU cc_start: 0.8807 (pt0) cc_final: 0.8350 (pm20) REVERT: D 15 ASN cc_start: 0.7898 (m-40) cc_final: 0.7290 (p0) REVERT: D 59 ARG cc_start: 0.7983 (mpp80) cc_final: 0.7638 (mpp80) REVERT: D 134 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: D 143 HIS cc_start: 0.8591 (t70) cc_final: 0.8118 (t-90) REVERT: D 195 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7523 (m-40) REVERT: D 220 MET cc_start: 0.8600 (mmm) cc_final: 0.7258 (mmm) REVERT: D 223 ASP cc_start: 0.8675 (t70) cc_final: 0.8084 (t0) REVERT: D 251 GLU cc_start: 0.7708 (tp30) cc_final: 0.7344 (tp30) REVERT: D 266 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7596 (tm-30) REVERT: E 71 GLU cc_start: 0.8848 (mp0) cc_final: 0.8549 (mp0) REVERT: E 237 THR cc_start: 0.9276 (t) cc_final: 0.8909 (p) REVERT: E 258 ASP cc_start: 0.8289 (m-30) cc_final: 0.7891 (m-30) REVERT: F 3 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7204 (mm-30) REVERT: F 7 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7503 (mt-10) REVERT: F 11 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8325 (tt) REVERT: F 130 ARG cc_start: 0.7944 (mmp-170) cc_final: 0.7645 (mmp80) REVERT: F 134 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 149 TYR cc_start: 0.6299 (t80) cc_final: 0.5921 (m-80) REVERT: F 220 MET cc_start: 0.7996 (tpt) cc_final: 0.7356 (mmm) REVERT: G 65 ASP cc_start: 0.8517 (t0) cc_final: 0.7990 (m-30) REVERT: G 113 MET cc_start: 0.6687 (mtm) cc_final: 0.6203 (mtp) REVERT: G 205 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8521 (mt-10) REVERT: H 7 GLU cc_start: 0.8808 (pt0) cc_final: 0.8350 (pm20) REVERT: H 15 ASN cc_start: 0.7895 (m-40) cc_final: 0.7289 (p0) REVERT: H 59 ARG cc_start: 0.7981 (mpp80) cc_final: 0.7637 (mpp80) REVERT: H 134 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: H 143 HIS cc_start: 0.8593 (t70) cc_final: 0.8119 (t-90) REVERT: H 195 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7526 (m-40) REVERT: H 220 MET cc_start: 0.8596 (mmm) cc_final: 0.7254 (mmm) REVERT: H 223 ASP cc_start: 0.8670 (t70) cc_final: 0.8080 (t0) REVERT: H 251 GLU cc_start: 0.7705 (tp30) cc_final: 0.7342 (tp30) REVERT: H 266 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7666 (tm-30) outliers start: 36 outliers final: 23 residues processed: 245 average time/residue: 0.2955 time to fit residues: 111.3569 Evaluate side-chains 238 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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 123 ASN Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 26 THR 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 195 ASN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 195 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 51 optimal weight: 30.0000 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 167 GLN E 52 ASN E 123 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.144970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.101774 restraints weight = 44147.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104828 restraints weight = 20709.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.106550 restraints weight = 13164.087| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 19826 Z= 0.260 Angle : 0.973 59.200 27584 Z= 0.599 Chirality : 0.046 1.195 3002 Planarity : 0.005 0.117 3000 Dihedral : 21.925 80.843 3740 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 1.87 % Allowed : 17.85 % Favored : 80.28 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.87 (0.20), residues: 1936 helix: 1.75 (0.19), residues: 824 sheet: 0.37 (0.29), residues: 360 loop : -0.59 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 208 HIS 0.007 0.001 HIS H 161 PHE 0.021 0.001 PHE G 21 TYR 0.010 0.001 TYR G 85 ARG 0.013 0.000 ARG H 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.43 seconds wall clock time: 63 minutes 55.45 seconds (3835.45 seconds total)