Starting phenix.real_space_refine on Fri Feb 6 10:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.map" model { file = "/net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y0l_72395/02_2026/9y0l_72395.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 15685 2.51 5 N 4101 2.21 5 O 4548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24452 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1852 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1696 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 219} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1789 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 10, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 225} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1480 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1575 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "J" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1433 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "K" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1494 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1670 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 70 Chain: "M" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1497 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "e" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 941 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.51, per 1000 atoms: 0.23 Number of scatterers: 24452 At special positions: 0 Unit cell: (134.144, 134.144, 98.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 4548 8.00 N 4101 7.00 C 15685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 48 " distance=2.04 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 160 " distance=2.05 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: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 42 sheets defined 41.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.774A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.628A pdb=" N LEU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.546A pdb=" N VAL A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.949A pdb=" N ILE A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.741A pdb=" N GLU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.723A pdb=" N PHE B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.756A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.544A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 217 through 221 removed outlier: 3.891A pdb=" N GLY C 220 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.540A pdb=" N ILE D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.685A pdb=" N VAL D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.583A pdb=" N ASN D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 200 through 204' Processing helix chain 'D' and resid 218 through 234 removed outlier: 3.598A pdb=" N THR D 234 " --> pdb=" O ASP D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 31 Processing helix chain 'E' and resid 81 through 103 Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 175 through 187 removed outlier: 4.080A pdb=" N ALA E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 233 through 243 Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.590A pdb=" N LYS F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.729A pdb=" N SER F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.739A pdb=" N PHE F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 179' Processing helix chain 'F' and resid 182 through 199 Processing helix chain 'F' and resid 224 through 237 Processing helix chain 'G' and resid 7 through 11 removed outlier: 3.888A pdb=" N SER G 11 " --> pdb=" O TYR G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.557A pdb=" N GLU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 4.068A pdb=" N LYS G 57 " --> pdb=" O ASN G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 124 Processing helix chain 'G' and resid 171 through 180 Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.940A pdb=" N ILE G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.690A pdb=" N LEU G 212 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN G 213 " --> pdb=" O ASN G 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 213' Processing helix chain 'G' and resid 233 through 250 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 48 through 70 Processing helix chain 'H' and resid 120 through 124 removed outlier: 3.902A pdb=" N ASN H 123 " --> pdb=" O ASP H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'H' and resid 186 through 194 removed outlier: 4.106A pdb=" N SER H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 220 Processing helix chain 'I' and resid -37 through -28 Processing helix chain 'I' and resid -21 through -11 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.575A pdb=" N CYS I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.890A pdb=" N ALA I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 removed outlier: 4.036A pdb=" N ALA I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 81 Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.520A pdb=" N PHE J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.817A pdb=" N LEU J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET J 162 " --> pdb=" O GLN J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 184 Processing helix chain 'K' and resid 50 through 73 removed outlier: 3.819A pdb=" N GLU K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 96 Processing helix chain 'K' and resid 135 through 147 removed outlier: 3.535A pdb=" N ALA K 141 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid -51 through -41 Processing helix chain 'L' and resid -21 through -19 No H-bonds generated for 'chain 'L' and resid -21 through -19' Processing helix chain 'L' and resid -18 through -9 Processing helix chain 'L' and resid 48 through 70 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.585A pdb=" N TYR L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 142 removed outlier: 3.624A pdb=" N ALA L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 164 Processing helix chain 'M' and resid 85 through 108 Processing helix chain 'M' and resid 112 through 127 removed outlier: 3.672A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 182 removed outlier: 3.596A pdb=" N LEU M 174 " --> pdb=" O SER M 170 " (cutoff:3.500A) Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 194 through 212 Processing helix chain 'N' and resid 57 through 78 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 87 through 106 removed outlier: 3.602A pdb=" N TYR N 91 " --> pdb=" O THR N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 130 removed outlier: 3.604A pdb=" N ASN N 129 " --> pdb=" O ASN N 126 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL N 130 " --> pdb=" O ASP N 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 126 through 130' Processing helix chain 'N' and resid 180 through 193 removed outlier: 4.056A pdb=" N PHE N 184 " --> pdb=" O TYR N 180 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU N 186 " --> pdb=" O ARG N 182 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR N 187 " --> pdb=" O TYR N 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 216 Processing helix chain 'e' and resid 32 through 39 Processing helix chain 'e' and resid 41 through 56 Processing helix chain 'e' and resid 57 through 74 removed outlier: 3.893A pdb=" N VAL e 61 " --> pdb=" O GLY e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 91 Processing helix chain 'e' and resid 113 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.734A pdb=" N ILE A 233 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 242 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 149 removed outlier: 4.204A pdb=" N LEU A 157 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 159 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.625A pdb=" N VAL B 163 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 43 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.621A pdb=" N ILE B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 137 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 37 Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.388A pdb=" N ILE C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 216 Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'D' and resid 70 through 72 removed outlier: 3.886A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 154 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 37 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.701A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.044A pdb=" N SER E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS E 76 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP E 71 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 48 removed outlier: 3.805A pdb=" N ALA F 37 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 158 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.846A pdb=" N ILE F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY F 71 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 73 " --> pdb=" O MET F 133 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET F 133 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 212 through 215 removed outlier: 7.380A pdb=" N VAL F 213 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP F 220 " --> pdb=" O VAL F 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 165 through 168 removed outlier: 3.857A pdb=" N ILE G 221 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS G 48 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER G 219 " --> pdb=" O CYS G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.734A pdb=" N TYR G 161 " --> pdb=" O CYS G 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 114 through 117 removed outlier: 3.561A pdb=" N GLU H 240 " --> pdb=" O ASN H 114 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 238 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE H 237 " --> pdb=" O THR H 234 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 229 " --> pdb=" O CYS H 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE H 3 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 182 " --> pdb=" O ILE H 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 35 through 38 removed outlier: 3.864A pdb=" N VAL H 43 " --> pdb=" O ASN H 35 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE H 37 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU H 164 " --> pdb=" O LYS H 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.840A pdb=" N ALA I 11 " --> pdb=" O CYS I 8 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU I 14 " --> pdb=" O CYS I 176 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS I 176 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL I 177 " --> pdb=" O GLN I 184 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN I 184 " --> pdb=" O VAL I 177 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.292A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.292A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP I 42 " --> pdb=" O GLY I 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 150 through 153 removed outlier: 3.570A pdb=" N VAL J 150 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN J 152 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP J 26 " --> pdb=" O CYS J 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS J 207 " --> pdb=" O THR J 204 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AD1, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.270A pdb=" N VAL J 51 " --> pdb=" O MET J 47 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE J 110 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA J 136 " --> pdb=" O CYS J 144 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS J 144 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.962A pdb=" N PHE K 12 " --> pdb=" O GLY K 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA K 17 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 36 through 39 removed outlier: 4.233A pdb=" N LYS K 43 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 36 through 39 removed outlier: 4.233A pdb=" N LYS K 43 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS K 44 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA K 105 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 125 through 128 removed outlier: 3.529A pdb=" N HIS L 178 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 34 through 36 removed outlier: 3.570A pdb=" N SER L 102 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 98 through 100 Processing sheet with id=AD8, first strand: chain 'M' and resid 41 through 43 removed outlier: 3.622A pdb=" N SER M 164 " --> pdb=" O GLY M 42 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 53 through 54 removed outlier: 3.517A pdb=" N ALA M 53 " --> pdb=" O LEU M 221 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 57 through 58 removed outlier: 7.171A pdb=" N LEU M 57 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 72 through 75 removed outlier: 5.616A pdb=" N LYS M 73 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE M 80 " --> pdb=" O LYS M 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 224 through 226 removed outlier: 3.782A pdb=" N GLY M 229 " --> pdb=" O ASP M 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AE5, first strand: chain 'N' and resid 176 through 177 removed outlier: 3.566A pdb=" N ILE N 176 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA N 14 " --> pdb=" O ILE N 176 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE N 224 " --> pdb=" O PRO N 239 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE N 226 " --> pdb=" O GLU N 237 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 44 through 47 removed outlier: 3.603A pdb=" N MET N 52 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE N 46 " --> pdb=" O THR N 50 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE N 115 " --> pdb=" O GLY N 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE N 163 " --> pdb=" O PHE N 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE N 171 " --> pdb=" O PHE N 163 " (cutoff:3.500A) 1293 hydrogen bonds defined for protein. 3666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4031 1.31 - 1.44: 6654 1.44 - 1.58: 14038 1.58 - 1.72: 3 1.72 - 1.85: 168 Bond restraints: 24894 Sorted by residual: bond pdb=" C GLU B 120 " pdb=" O GLU B 120 " ideal model delta sigma weight residual 1.236 1.170 0.067 1.15e-02 7.56e+03 3.35e+01 bond pdb=" N ILE I 113 " pdb=" CA ILE I 113 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.60e+00 bond pdb=" N ASP N 26 " pdb=" CA ASP N 26 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.40e-02 5.10e+03 7.82e+00 bond pdb=" N ARG K 95 " pdb=" CA ARG K 95 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.35e-02 5.49e+03 7.34e+00 bond pdb=" N ASP G 150 " pdb=" CA ASP G 150 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.20e-02 6.94e+03 6.93e+00 ... (remaining 24889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 33063 2.67 - 5.33: 640 5.33 - 8.00: 63 8.00 - 10.66: 8 10.66 - 13.33: 1 Bond angle restraints: 33775 Sorted by residual: angle pdb=" CA GLU B 120 " pdb=" C GLU B 120 " pdb=" O GLU B 120 " ideal model delta sigma weight residual 121.00 115.10 5.90 1.05e+00 9.07e-01 3.16e+01 angle pdb=" N GLU B 120 " pdb=" CA GLU B 120 " pdb=" CB GLU B 120 " ideal model delta sigma weight residual 109.91 117.63 -7.72 1.46e+00 4.69e-01 2.79e+01 angle pdb=" N GLU B 120 " pdb=" CA GLU B 120 " pdb=" C GLU B 120 " ideal model delta sigma weight residual 110.97 105.33 5.64 1.09e+00 8.42e-01 2.67e+01 angle pdb=" N GLU D 24 " pdb=" CA GLU D 24 " pdb=" CB GLU D 24 " ideal model delta sigma weight residual 110.39 118.23 -7.84 1.66e+00 3.63e-01 2.23e+01 angle pdb=" CA ASP L 105 " pdb=" CB ASP L 105 " pdb=" CG ASP L 105 " ideal model delta sigma weight residual 112.60 117.24 -4.64 1.00e+00 1.00e+00 2.16e+01 ... (remaining 33770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13431 17.97 - 35.94: 1112 35.94 - 53.92: 160 53.92 - 71.89: 31 71.89 - 89.86: 25 Dihedral angle restraints: 14759 sinusoidal: 5360 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS I 156 " pdb=" SG CYS I 156 " pdb=" SG CYS I 160 " pdb=" CB CYS I 160 " ideal model delta sinusoidal sigma weight residual -86.00 -130.68 44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 137.28 -44.28 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CA TRP G 220 " pdb=" C TRP G 220 " pdb=" N ILE G 221 " pdb=" CA ILE G 221 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 14756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2849 0.047 - 0.094: 777 0.094 - 0.141: 237 0.141 - 0.188: 56 0.188 - 0.235: 5 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CB ILE G 232 " pdb=" CA ILE G 232 " pdb=" CG1 ILE G 232 " pdb=" CG2 ILE G 232 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA MET L 111 " pdb=" N MET L 111 " pdb=" C MET L 111 " pdb=" CB MET L 111 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE H 139 " pdb=" CA ILE H 139 " pdb=" CG1 ILE H 139 " pdb=" CG2 ILE H 139 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3921 not shown) Planarity restraints: 4293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L -25 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO L -24 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO L -24 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L -24 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE e 13 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C PHE e 13 " 0.052 2.00e-02 2.50e+03 pdb=" O PHE e 13 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS e 14 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 220 " 0.024 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP G 220 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP G 220 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 220 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 220 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 220 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 220 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 220 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 220 " 0.000 2.00e-02 2.50e+03 ... (remaining 4290 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 269 2.65 - 3.21: 22516 3.21 - 3.78: 36847 3.78 - 4.34: 50555 4.34 - 4.90: 86952 Nonbonded interactions: 197139 Sorted by model distance: nonbonded pdb=" O TYR L -14 " pdb=" OG1 THR L -11 " model vdw 2.088 3.040 nonbonded pdb=" O ILE M 123 " pdb=" OG SER M 126 " model vdw 2.243 3.040 nonbonded pdb=" O VAL I 80 " pdb=" OG1 THR I 84 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR G 107 " pdb=" OD1 ASN H 131 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLN F 117 " pdb=" NZ LYS F 118 " model vdw 2.260 3.120 ... (remaining 197134 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 4.230 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.400 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 0.006 0.068 24897 Z= 0.267 Angle : 0.864 13.327 33781 Z= 0.465 Chirality : 0.050 0.235 3924 Planarity : 0.006 0.101 4293 Dihedral : 13.755 89.861 8718 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.08 % Allowed : 0.40 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3140 helix: 1.16 (0.14), residues: 1214 sheet: -1.92 (0.19), residues: 635 loop : -1.74 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.042 0.002 TYR N 86 PHE 0.022 0.002 PHE F 58 TRP 0.048 0.002 TRP G 220 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00597 (24894) covalent geometry : angle 0.86336 (33775) SS BOND : bond 0.00981 ( 3) SS BOND : angle 2.44862 ( 6) hydrogen bonds : bond 0.15865 ( 1287) hydrogen bonds : angle 7.02656 ( 3666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 523 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ILE cc_start: 0.7325 (mm) cc_final: 0.6957 (mm) REVERT: E 156 TRP cc_start: 0.7538 (m100) cc_final: 0.7336 (m100) REVERT: H 210 ILE cc_start: 0.7799 (tt) cc_final: 0.7418 (pt) REVERT: M 56 ARG cc_start: 0.7104 (ttp-170) cc_final: 0.6822 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 525 average time/residue: 0.4708 time to fit residues: 296.0768 Evaluate side-chains 383 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain M residue 194 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN D 159 GLN E 97 ASN E 186 ASN E 227 GLN F 89 GLN F 139 ASN G 67 ASN G 157 ASN G 211 ASN H 190 GLN H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS J 118 HIS J 182 GLN K 11 ASN L 89 GLN L 178 HIS M 179 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136524 restraints weight = 31077.559| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.21 r_work: 0.3500 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24897 Z= 0.131 Angle : 0.554 10.558 33781 Z= 0.297 Chirality : 0.044 0.217 3924 Planarity : 0.004 0.056 4293 Dihedral : 4.103 24.445 3469 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.65 % Allowed : 11.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3140 helix: 1.99 (0.14), residues: 1246 sheet: -1.53 (0.20), residues: 638 loop : -1.59 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 190 TYR 0.039 0.001 TYR N 86 PHE 0.027 0.002 PHE e 13 TRP 0.037 0.002 TRP G 220 HIS 0.004 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00295 (24894) covalent geometry : angle 0.55368 (33775) SS BOND : bond 0.00731 ( 3) SS BOND : angle 1.92773 ( 6) hydrogen bonds : bond 0.03560 ( 1287) hydrogen bonds : angle 5.10812 ( 3666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 417 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 SER cc_start: 0.7729 (p) cc_final: 0.7510 (t) REVERT: A 156 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 207 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6060 (t0) REVERT: C 15 GLU cc_start: 0.7094 (pm20) cc_final: 0.6770 (pm20) REVERT: C 22 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 183 MET cc_start: 0.8130 (ttp) cc_final: 0.7666 (ttm) REVERT: D 37 SER cc_start: 0.7199 (t) cc_final: 0.6191 (p) REVERT: E 156 TRP cc_start: 0.8008 (m100) cc_final: 0.7250 (m100) REVERT: F 119 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7288 (t0) REVERT: G 73 ASN cc_start: 0.7167 (m-40) cc_final: 0.6851 (p0) REVERT: G 76 ILE cc_start: 0.7640 (mt) cc_final: 0.7369 (mt) REVERT: I -14 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6357 (mp) REVERT: I -11 LYS cc_start: 0.6460 (mttm) cc_final: 0.6153 (mtpp) REVERT: I 33 LYS cc_start: 0.6184 (mptt) cc_final: 0.5922 (tppt) REVERT: I 64 GLU cc_start: 0.6830 (tp30) cc_final: 0.6500 (tp30) REVERT: I 70 THR cc_start: 0.7945 (m) cc_final: 0.7735 (p) REVERT: I 122 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7908 (pp) REVERT: J 150 VAL cc_start: 0.7972 (p) cc_final: 0.7666 (t) REVERT: K 179 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6429 (tm-30) REVERT: L 45 MET cc_start: 0.7378 (mtp) cc_final: 0.6892 (mtp) REVERT: L 102 SER cc_start: 0.7958 (t) cc_final: 0.7349 (m) REVERT: L 104 TYR cc_start: 0.6660 (t80) cc_final: 0.6441 (t80) REVERT: L 111 MET cc_start: 0.8555 (tpp) cc_final: 0.8033 (tpp) REVERT: L 153 VAL cc_start: 0.7475 (t) cc_final: 0.7263 (p) REVERT: M 71 ILE cc_start: 0.7130 (mm) cc_final: 0.6911 (mm) REVERT: M 90 LYS cc_start: 0.6618 (tppt) cc_final: 0.6406 (mptt) REVERT: N 31 TYR cc_start: 0.6894 (t80) cc_final: 0.6559 (t80) REVERT: e 23 ASP cc_start: 0.5370 (t0) cc_final: 0.5127 (t0) REVERT: e 122 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.4205 (ppp) outliers start: 66 outliers final: 19 residues processed: 451 average time/residue: 0.4541 time to fit residues: 246.2806 Evaluate side-chains 387 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 362 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue -14 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 272 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 309 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 chunk 149 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN E 186 ASN G 67 ASN H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS K 11 ASN N 89 GLN e 37 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118681 restraints weight = 32838.988| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.09 r_work: 0.3427 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24897 Z= 0.164 Angle : 0.559 11.843 33781 Z= 0.300 Chirality : 0.044 0.261 3924 Planarity : 0.004 0.064 4293 Dihedral : 4.068 26.998 3467 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 2.85 % Allowed : 14.72 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3140 helix: 2.16 (0.14), residues: 1249 sheet: -1.52 (0.19), residues: 697 loop : -1.29 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 88 TYR 0.032 0.002 TYR N 86 PHE 0.020 0.002 PHE A 158 TRP 0.041 0.002 TRP G 220 HIS 0.005 0.001 HIS G 112 Details of bonding type rmsd covalent geometry : bond 0.00378 (24894) covalent geometry : angle 0.55801 (33775) SS BOND : bond 0.00774 ( 3) SS BOND : angle 1.99876 ( 6) hydrogen bonds : bond 0.03642 ( 1287) hydrogen bonds : angle 4.74392 ( 3666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 411 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6456 (t0) REVERT: C 22 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 64 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8038 (mmtm) REVERT: C 183 MET cc_start: 0.8568 (ttp) cc_final: 0.8105 (ttm) REVERT: D 37 SER cc_start: 0.7933 (t) cc_final: 0.7063 (p) REVERT: D 67 GLU cc_start: 0.8642 (mp0) cc_final: 0.8435 (mp0) REVERT: E 72 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: F 18 ARG cc_start: 0.8127 (ptm160) cc_final: 0.7036 (ptm-80) REVERT: F 36 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7209 (m) REVERT: F 118 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8012 (mmtt) REVERT: F 119 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7751 (t0) REVERT: G 73 ASN cc_start: 0.7714 (m-40) cc_final: 0.7292 (p0) REVERT: G 76 ILE cc_start: 0.8343 (mt) cc_final: 0.8068 (mt) REVERT: H 194 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: H 201 MET cc_start: 0.7565 (ppp) cc_final: 0.7163 (ppp) REVERT: H 205 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: H 241 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.4969 (p90) REVERT: I -14 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6845 (mp) REVERT: I 64 GLU cc_start: 0.7669 (tp30) cc_final: 0.7345 (tp30) REVERT: J 115 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6940 (mmtt) REVERT: L 45 MET cc_start: 0.7888 (mtp) cc_final: 0.7270 (mtp) REVERT: L 102 SER cc_start: 0.8254 (t) cc_final: 0.7784 (m) REVERT: L 111 MET cc_start: 0.8685 (tpp) cc_final: 0.8324 (tpp) REVERT: N 31 TYR cc_start: 0.7144 (t80) cc_final: 0.6908 (t80) REVERT: N 76 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7964 (mp) REVERT: N 84 ASP cc_start: 0.8048 (m-30) cc_final: 0.7636 (m-30) REVERT: N 201 GLU cc_start: 0.8143 (mp0) cc_final: 0.7623 (mp0) REVERT: N 213 LEU cc_start: 0.7338 (mm) cc_final: 0.7073 (mm) outliers start: 71 outliers final: 29 residues processed: 454 average time/residue: 0.4693 time to fit residues: 255.1447 Evaluate side-chains 400 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 361 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain I residue -14 LEU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 246 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN G 67 ASN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 HIS H 190 GLN H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN K 72 ASN K 96 ASN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107183 restraints weight = 33759.546| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.07 r_work: 0.3226 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 24897 Z= 0.288 Angle : 0.689 11.619 33781 Z= 0.366 Chirality : 0.049 0.246 3924 Planarity : 0.005 0.064 4293 Dihedral : 4.625 27.646 3467 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 4.95 % Allowed : 16.08 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3140 helix: 1.70 (0.14), residues: 1251 sheet: -1.75 (0.18), residues: 704 loop : -1.49 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 93 TYR 0.039 0.002 TYR J 98 PHE 0.025 0.003 PHE F 160 TRP 0.051 0.003 TRP G 220 HIS 0.006 0.001 HIS K 132 Details of bonding type rmsd covalent geometry : bond 0.00701 (24894) covalent geometry : angle 0.68890 (33775) SS BOND : bond 0.00835 ( 3) SS BOND : angle 2.24859 ( 6) hydrogen bonds : bond 0.04657 ( 1287) hydrogen bonds : angle 5.09529 ( 3666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 390 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 248 GLU cc_start: 0.7058 (mp0) cc_final: 0.6857 (mp0) REVERT: B 7 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7094 (p) REVERT: B 135 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7272 (tt) REVERT: B 207 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6559 (t0) REVERT: C 8 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6779 (mtp85) REVERT: C 231 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7082 (mp0) REVERT: D 13 ASP cc_start: 0.7909 (t0) cc_final: 0.7703 (t0) REVERT: D 37 SER cc_start: 0.7751 (t) cc_final: 0.6881 (p) REVERT: D 67 GLU cc_start: 0.8630 (mp0) cc_final: 0.8375 (mp0) REVERT: E 28 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6390 (mp) REVERT: E 118 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: F 36 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7044 (m) REVERT: G 73 ASN cc_start: 0.8119 (m-40) cc_final: 0.7283 (p0) REVERT: H 123 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7494 (t0) REVERT: I 64 GLU cc_start: 0.7475 (tp30) cc_final: 0.7139 (tp30) REVERT: J 48 ASN cc_start: 0.8415 (t0) cc_final: 0.8110 (t0) REVERT: J 87 GLU cc_start: 0.8312 (mp0) cc_final: 0.8013 (mp0) REVERT: J 115 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7248 (mmmt) REVERT: J 157 GLU cc_start: 0.8548 (mp0) cc_final: 0.8322 (mp0) REVERT: J 162 MET cc_start: 0.7980 (mtm) cc_final: 0.7485 (mpt) REVERT: J 212 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7343 (mmmt) REVERT: L 38 ASN cc_start: 0.7266 (t0) cc_final: 0.7033 (t160) REVERT: L 45 MET cc_start: 0.8072 (mtp) cc_final: 0.7432 (mtp) REVERT: L 102 SER cc_start: 0.8279 (t) cc_final: 0.7837 (m) REVERT: L 111 MET cc_start: 0.8447 (tpp) cc_final: 0.8147 (tpp) REVERT: M 41 ILE cc_start: 0.6685 (tt) cc_final: 0.6452 (pp) REVERT: M 231 ASN cc_start: 0.5931 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: N 22 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: N 26 ASP cc_start: 0.7744 (p0) cc_final: 0.7474 (p0) REVERT: N 201 GLU cc_start: 0.8110 (mp0) cc_final: 0.7602 (mp0) REVERT: N 217 ASP cc_start: 0.7882 (t0) cc_final: 0.7589 (t0) outliers start: 123 outliers final: 46 residues processed: 472 average time/residue: 0.5048 time to fit residues: 284.3230 Evaluate side-chains 412 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 295 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN E 227 GLN F 217 ASN G 67 ASN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L -12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111074 restraints weight = 33110.301| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.12 r_work: 0.3280 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24897 Z= 0.147 Angle : 0.559 9.066 33781 Z= 0.301 Chirality : 0.044 0.203 3924 Planarity : 0.004 0.067 4293 Dihedral : 4.291 25.619 3467 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 3.94 % Allowed : 19.18 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3140 helix: 2.03 (0.14), residues: 1251 sheet: -1.55 (0.18), residues: 694 loop : -1.45 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 88 TYR 0.034 0.001 TYR J 98 PHE 0.022 0.002 PHE J 106 TRP 0.042 0.002 TRP G 220 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00354 (24894) covalent geometry : angle 0.55861 (33775) SS BOND : bond 0.00808 ( 3) SS BOND : angle 2.35274 ( 6) hydrogen bonds : bond 0.03586 ( 1287) hydrogen bonds : angle 4.73811 ( 3666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 389 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 106 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 7 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.6807 (p) REVERT: B 207 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6408 (t0) REVERT: C 102 ASN cc_start: 0.8725 (t0) cc_final: 0.8136 (t0) REVERT: C 231 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6991 (mt-10) REVERT: D 11 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.7712 (p) REVERT: D 13 ASP cc_start: 0.7901 (t0) cc_final: 0.7604 (t0) REVERT: D 37 SER cc_start: 0.7745 (t) cc_final: 0.6799 (p) REVERT: D 67 GLU cc_start: 0.8623 (mp0) cc_final: 0.8411 (mp0) REVERT: D 97 ASN cc_start: 0.7154 (m-40) cc_final: 0.6935 (m-40) REVERT: D 139 ASN cc_start: 0.9008 (t0) cc_final: 0.8767 (t0) REVERT: E 28 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6452 (mp) REVERT: E 72 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: E 118 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: G 20 ARG cc_start: 0.8509 (ptm160) cc_final: 0.8024 (ptm-80) REVERT: G 73 ASN cc_start: 0.7995 (m-40) cc_final: 0.7277 (p0) REVERT: G 76 ILE cc_start: 0.8368 (mt) cc_final: 0.8101 (mt) REVERT: G 103 TYR cc_start: 0.7078 (m-80) cc_final: 0.6426 (t80) REVERT: G 155 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: H 172 SER cc_start: 0.7702 (m) cc_final: 0.6963 (t) REVERT: H 201 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6922 (ppp) REVERT: H 241 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5081 (p90) REVERT: I 64 GLU cc_start: 0.7547 (tp30) cc_final: 0.7242 (tp30) REVERT: I 86 GLU cc_start: 0.8747 (tp30) cc_final: 0.8511 (tp30) REVERT: J 48 ASN cc_start: 0.8305 (t0) cc_final: 0.7950 (t0) REVERT: J 115 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7411 (mmmt) REVERT: J 143 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7779 (ttpt) REVERT: J 162 MET cc_start: 0.8061 (mtm) cc_final: 0.7422 (mpt) REVERT: J 212 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7399 (mmmt) REVERT: L 38 ASN cc_start: 0.7269 (t0) cc_final: 0.7013 (t160) REVERT: L 45 MET cc_start: 0.7992 (mtp) cc_final: 0.7509 (mtp) REVERT: L 102 SER cc_start: 0.8228 (t) cc_final: 0.7817 (m) REVERT: L 111 MET cc_start: 0.8331 (tpp) cc_final: 0.8036 (tpp) REVERT: L 136 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: M 110 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: M 142 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: M 174 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7635 (mp) REVERT: N 26 ASP cc_start: 0.7716 (p0) cc_final: 0.7411 (p0) REVERT: N 121 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8418 (mm-40) REVERT: N 201 GLU cc_start: 0.8180 (mp0) cc_final: 0.7720 (mp0) REVERT: e 122 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.3884 (ppp) outliers start: 98 outliers final: 40 residues processed: 450 average time/residue: 0.5032 time to fit residues: 270.8938 Evaluate side-chains 412 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 268 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN F 217 ASN G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110042 restraints weight = 33319.822| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.13 r_work: 0.3265 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24897 Z= 0.175 Angle : 0.577 11.936 33781 Z= 0.308 Chirality : 0.045 0.250 3924 Planarity : 0.004 0.068 4293 Dihedral : 4.259 27.151 3467 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 4.02 % Allowed : 19.34 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3140 helix: 2.07 (0.14), residues: 1251 sheet: -1.53 (0.19), residues: 691 loop : -1.47 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 88 TYR 0.036 0.002 TYR J 98 PHE 0.020 0.002 PHE K 164 TRP 0.044 0.002 TRP G 220 HIS 0.008 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00426 (24894) covalent geometry : angle 0.57567 (33775) SS BOND : bond 0.00859 ( 3) SS BOND : angle 2.46695 ( 6) hydrogen bonds : bond 0.03680 ( 1287) hydrogen bonds : angle 4.70216 ( 3666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 376 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 106 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B 7 SER cc_start: 0.7214 (OUTLIER) cc_final: 0.6794 (p) REVERT: B 135 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7256 (tt) REVERT: B 207 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6277 (t0) REVERT: C 102 ASN cc_start: 0.8750 (t0) cc_final: 0.8142 (t0) REVERT: C 231 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7083 (mt-10) REVERT: D 13 ASP cc_start: 0.7955 (t0) cc_final: 0.7748 (t0) REVERT: D 37 SER cc_start: 0.7750 (t) cc_final: 0.6851 (p) REVERT: D 67 GLU cc_start: 0.8610 (mp0) cc_final: 0.8397 (mp0) REVERT: D 98 MET cc_start: 0.7859 (mmt) cc_final: 0.7491 (mmm) REVERT: D 139 ASN cc_start: 0.9012 (t0) cc_final: 0.8780 (t0) REVERT: D 180 MET cc_start: 0.7472 (mtm) cc_final: 0.7125 (mtp) REVERT: E 28 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6461 (mp) REVERT: E 118 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: F 36 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7106 (m) REVERT: F 160 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: G 20 ARG cc_start: 0.8571 (ptm160) cc_final: 0.8247 (ptm160) REVERT: G 73 ASN cc_start: 0.8010 (m-40) cc_final: 0.7273 (p0) REVERT: G 155 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: H 172 SER cc_start: 0.7784 (m) cc_final: 0.7019 (t) REVERT: H 201 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6833 (ppp) REVERT: H 241 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5030 (p90) REVERT: I -24 ASN cc_start: 0.7628 (p0) cc_final: 0.7411 (p0) REVERT: I 64 GLU cc_start: 0.7558 (tp30) cc_final: 0.7236 (tp30) REVERT: I 86 GLU cc_start: 0.8813 (tp30) cc_final: 0.8465 (tp30) REVERT: J 48 ASN cc_start: 0.8350 (t0) cc_final: 0.7959 (t0) REVERT: J 143 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7710 (ttpt) REVERT: J 212 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7468 (mmmt) REVERT: L 38 ASN cc_start: 0.7289 (t0) cc_final: 0.7029 (t160) REVERT: L 45 MET cc_start: 0.8039 (mtp) cc_final: 0.7517 (mtp) REVERT: L 102 SER cc_start: 0.8229 (t) cc_final: 0.7817 (m) REVERT: L 111 MET cc_start: 0.8322 (tpp) cc_final: 0.8079 (tpp) REVERT: L 136 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: M 56 ARG cc_start: 0.6682 (ttp-170) cc_final: 0.6368 (tpp80) REVERT: M 110 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: M 125 TYR cc_start: 0.8127 (t80) cc_final: 0.7864 (t80) REVERT: M 142 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: N 26 ASP cc_start: 0.7705 (p0) cc_final: 0.7407 (p0) REVERT: N 84 ASP cc_start: 0.7835 (m-30) cc_final: 0.7481 (m-30) REVERT: N 201 GLU cc_start: 0.8142 (mp0) cc_final: 0.7648 (mp0) outliers start: 100 outliers final: 55 residues processed: 442 average time/residue: 0.4481 time to fit residues: 237.7688 Evaluate side-chains 417 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 187 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 309 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS G 157 ASN H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110789 restraints weight = 33213.163| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.14 r_work: 0.3285 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 24897 Z= 0.158 Angle : 0.579 16.222 33781 Z= 0.308 Chirality : 0.044 0.231 3924 Planarity : 0.004 0.068 4293 Dihedral : 4.213 25.460 3467 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 4.50 % Allowed : 19.58 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3140 helix: 2.12 (0.14), residues: 1250 sheet: -1.49 (0.18), residues: 699 loop : -1.46 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 88 TYR 0.037 0.001 TYR J 98 PHE 0.023 0.002 PHE J 106 TRP 0.043 0.002 TRP G 220 HIS 0.009 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00386 (24894) covalent geometry : angle 0.57457 (33775) SS BOND : bond 0.01911 ( 3) SS BOND : angle 5.18026 ( 6) hydrogen bonds : bond 0.03573 ( 1287) hydrogen bonds : angle 4.67267 ( 3666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 371 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 106 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 7 SER cc_start: 0.6709 (OUTLIER) cc_final: 0.6302 (p) REVERT: B 70 GLU cc_start: 0.8612 (tt0) cc_final: 0.8222 (tm-30) REVERT: B 135 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7231 (tt) REVERT: C 102 ASN cc_start: 0.8729 (t0) cc_final: 0.8124 (t0) REVERT: C 231 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7017 (mt-10) REVERT: D 13 ASP cc_start: 0.7914 (t0) cc_final: 0.7709 (t0) REVERT: D 37 SER cc_start: 0.7758 (t) cc_final: 0.6820 (p) REVERT: D 67 GLU cc_start: 0.8611 (mp0) cc_final: 0.8340 (mp0) REVERT: D 98 MET cc_start: 0.7873 (mmt) cc_final: 0.7536 (mmm) REVERT: D 139 ASN cc_start: 0.9078 (t0) cc_final: 0.8824 (t0) REVERT: D 180 MET cc_start: 0.7478 (mtm) cc_final: 0.7176 (mtp) REVERT: E 28 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6393 (mp) REVERT: F 36 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.7070 (m) REVERT: G 20 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8266 (ptm160) REVERT: G 73 ASN cc_start: 0.8000 (m-40) cc_final: 0.7266 (p0) REVERT: G 155 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: H 172 SER cc_start: 0.7779 (m) cc_final: 0.7034 (t) REVERT: H 194 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: H 201 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6833 (ppp) REVERT: H 241 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.4942 (p90) REVERT: I 64 GLU cc_start: 0.7599 (tp30) cc_final: 0.7265 (tp30) REVERT: I 86 GLU cc_start: 0.8805 (tp30) cc_final: 0.8506 (tp30) REVERT: J 48 ASN cc_start: 0.8368 (t0) cc_final: 0.8003 (t0) REVERT: J 115 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7417 (mmmt) REVERT: J 143 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7710 (ttpt) REVERT: J 162 MET cc_start: 0.7975 (mtm) cc_final: 0.7575 (mpt) REVERT: J 212 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7447 (mmmt) REVERT: K 178 TYR cc_start: 0.6031 (m-80) cc_final: 0.5484 (m-10) REVERT: L 38 ASN cc_start: 0.7332 (t0) cc_final: 0.7042 (t160) REVERT: L 45 MET cc_start: 0.8074 (mtp) cc_final: 0.7449 (mtp) REVERT: L 102 SER cc_start: 0.8216 (t) cc_final: 0.7813 (m) REVERT: L 111 MET cc_start: 0.8286 (tpp) cc_final: 0.8038 (tpp) REVERT: M 56 ARG cc_start: 0.6590 (ttp-170) cc_final: 0.6201 (tpp80) REVERT: M 110 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: M 142 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: N 26 ASP cc_start: 0.7681 (p0) cc_final: 0.7384 (p0) REVERT: N 73 ILE cc_start: 0.6822 (mm) cc_final: 0.6598 (mp) REVERT: N 84 ASP cc_start: 0.7878 (m-30) cc_final: 0.7515 (m-30) REVERT: N 201 GLU cc_start: 0.8123 (mp0) cc_final: 0.7622 (mp0) outliers start: 112 outliers final: 57 residues processed: 444 average time/residue: 0.4491 time to fit residues: 240.2470 Evaluate side-chains 419 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 187 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 217 optimal weight: 3.9990 chunk 169 optimal weight: 0.0270 chunk 207 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112300 restraints weight = 32747.552| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.24 r_work: 0.3254 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 24897 Z= 0.121 Angle : 0.561 16.683 33781 Z= 0.298 Chirality : 0.043 0.308 3924 Planarity : 0.004 0.068 4293 Dihedral : 4.104 24.444 3467 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 3.46 % Allowed : 20.99 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3140 helix: 2.25 (0.14), residues: 1253 sheet: -1.36 (0.19), residues: 697 loop : -1.41 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 88 TYR 0.036 0.001 TYR J 98 PHE 0.025 0.001 PHE H 200 TRP 0.040 0.002 TRP G 220 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00286 (24894) covalent geometry : angle 0.55738 (33775) SS BOND : bond 0.01903 ( 3) SS BOND : angle 4.90897 ( 6) hydrogen bonds : bond 0.03244 ( 1287) hydrogen bonds : angle 4.53610 ( 3666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 382 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 106 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7236 (mm-30) REVERT: B 7 SER cc_start: 0.6217 (OUTLIER) cc_final: 0.5813 (p) REVERT: B 63 PHE cc_start: 0.6263 (m-80) cc_final: 0.6057 (m-80) REVERT: B 70 GLU cc_start: 0.8503 (tt0) cc_final: 0.8076 (tm-30) REVERT: C 102 ASN cc_start: 0.8555 (t0) cc_final: 0.7987 (t0) REVERT: C 231 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6875 (mt-10) REVERT: D 11 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7444 (p) REVERT: D 13 ASP cc_start: 0.7858 (t0) cc_final: 0.7534 (t0) REVERT: D 37 SER cc_start: 0.7404 (t) cc_final: 0.6418 (p) REVERT: D 67 GLU cc_start: 0.8629 (mp0) cc_final: 0.8346 (mp0) REVERT: D 98 MET cc_start: 0.7711 (mmt) cc_final: 0.7402 (mmm) REVERT: D 139 ASN cc_start: 0.9028 (t0) cc_final: 0.8769 (t0) REVERT: D 180 MET cc_start: 0.7233 (mtm) cc_final: 0.6883 (mtp) REVERT: E 28 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5998 (mp) REVERT: E 136 SER cc_start: 0.8391 (p) cc_final: 0.8071 (m) REVERT: E 236 ASP cc_start: 0.8341 (m-30) cc_final: 0.7837 (p0) REVERT: G 20 ARG cc_start: 0.8387 (ptm160) cc_final: 0.7973 (ptm160) REVERT: G 38 LEU cc_start: 0.7568 (tt) cc_final: 0.7299 (tm) REVERT: G 73 ASN cc_start: 0.7931 (m-40) cc_final: 0.7118 (p0) REVERT: G 155 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: G 193 ILE cc_start: 0.7430 (mt) cc_final: 0.7180 (mp) REVERT: H 172 SER cc_start: 0.7565 (m) cc_final: 0.6871 (t) REVERT: H 201 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6520 (ppp) REVERT: H 241 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.4621 (p90) REVERT: I 64 GLU cc_start: 0.7257 (tp30) cc_final: 0.6902 (tp30) REVERT: J 48 ASN cc_start: 0.8274 (t0) cc_final: 0.7931 (t0) REVERT: J 143 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7535 (ttpt) REVERT: J 162 MET cc_start: 0.7900 (mtm) cc_final: 0.7475 (mpt) REVERT: J 212 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7343 (mmmt) REVERT: K 178 TYR cc_start: 0.5583 (m-80) cc_final: 0.5262 (m-10) REVERT: L 38 ASN cc_start: 0.7136 (t0) cc_final: 0.6898 (t160) REVERT: L 45 MET cc_start: 0.7936 (mtp) cc_final: 0.7407 (mtp) REVERT: L 102 SER cc_start: 0.8075 (t) cc_final: 0.7665 (m) REVERT: L 111 MET cc_start: 0.8285 (tpp) cc_final: 0.8069 (tpp) REVERT: M 110 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: M 142 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: M 146 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7087 (ttpp) REVERT: N 22 MET cc_start: 0.7986 (ptm) cc_final: 0.7634 (ptm) REVERT: N 26 ASP cc_start: 0.7652 (p0) cc_final: 0.7341 (p0) REVERT: N 38 GLN cc_start: 0.7922 (mt0) cc_final: 0.7676 (mt0) REVERT: N 84 ASP cc_start: 0.7672 (m-30) cc_final: 0.7203 (m-30) REVERT: N 201 GLU cc_start: 0.7980 (mp0) cc_final: 0.7531 (mp0) REVERT: e 122 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.3870 (pp-130) outliers start: 86 outliers final: 39 residues processed: 435 average time/residue: 0.4786 time to fit residues: 250.3347 Evaluate side-chains 390 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 341 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 187 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 268 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 221 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN E 227 GLN G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN N 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111808 restraints weight = 32699.815| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.18 r_work: 0.3256 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 24897 Z= 0.133 Angle : 0.566 16.006 33781 Z= 0.299 Chirality : 0.043 0.192 3924 Planarity : 0.004 0.069 4293 Dihedral : 4.066 25.340 3467 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 3.38 % Allowed : 21.27 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3140 helix: 2.32 (0.14), residues: 1252 sheet: -1.34 (0.18), residues: 699 loop : -1.41 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 88 TYR 0.039 0.001 TYR J 98 PHE 0.023 0.001 PHE H 200 TRP 0.041 0.002 TRP G 220 HIS 0.008 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00320 (24894) covalent geometry : angle 0.56242 (33775) SS BOND : bond 0.01818 ( 3) SS BOND : angle 4.65816 ( 6) hydrogen bonds : bond 0.03280 ( 1287) hydrogen bonds : angle 4.50136 ( 3666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 360 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 106 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 7 SER cc_start: 0.6173 (OUTLIER) cc_final: 0.5815 (p) REVERT: B 63 PHE cc_start: 0.6179 (m-80) cc_final: 0.5947 (m-80) REVERT: B 135 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6793 (tt) REVERT: C 102 ASN cc_start: 0.8529 (t0) cc_final: 0.7961 (t0) REVERT: C 231 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6964 (mt-10) REVERT: D 11 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7452 (p) REVERT: D 13 ASP cc_start: 0.7861 (t0) cc_final: 0.7553 (t0) REVERT: D 37 SER cc_start: 0.7446 (t) cc_final: 0.6421 (p) REVERT: D 67 GLU cc_start: 0.8640 (mp0) cc_final: 0.8361 (mp0) REVERT: D 98 MET cc_start: 0.7713 (mmt) cc_final: 0.7362 (mmm) REVERT: D 139 ASN cc_start: 0.8990 (t0) cc_final: 0.8735 (t0) REVERT: E 28 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.6024 (mp) REVERT: E 236 ASP cc_start: 0.8318 (m-30) cc_final: 0.7873 (p0) REVERT: G 38 LEU cc_start: 0.7541 (tt) cc_final: 0.7257 (tm) REVERT: G 73 ASN cc_start: 0.7956 (m-40) cc_final: 0.7114 (p0) REVERT: G 155 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: H 163 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: H 172 SER cc_start: 0.7579 (m) cc_final: 0.6870 (t) REVERT: H 201 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6528 (ppp) REVERT: H 241 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.4473 (p90) REVERT: I 36 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6325 (t80) REVERT: I 64 GLU cc_start: 0.7282 (tp30) cc_final: 0.6991 (tp30) REVERT: I 85 GLN cc_start: 0.7949 (mt0) cc_final: 0.7699 (mt0) REVERT: J 48 ASN cc_start: 0.8241 (t0) cc_final: 0.7917 (t0) REVERT: J 143 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7511 (ttpt) REVERT: J 162 MET cc_start: 0.7928 (mtm) cc_final: 0.7490 (mpt) REVERT: J 212 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7344 (mmmt) REVERT: K 178 TYR cc_start: 0.5508 (m-80) cc_final: 0.5083 (m-10) REVERT: L 38 ASN cc_start: 0.7119 (t0) cc_final: 0.6897 (t160) REVERT: L 45 MET cc_start: 0.7944 (mtp) cc_final: 0.7580 (mtp) REVERT: L 102 SER cc_start: 0.8083 (t) cc_final: 0.7673 (m) REVERT: L 111 MET cc_start: 0.8267 (tpp) cc_final: 0.8051 (tpp) REVERT: M 50 ILE cc_start: 0.7194 (mt) cc_final: 0.6950 (mt) REVERT: M 110 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: M 142 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: M 146 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7140 (ttpp) REVERT: N 22 MET cc_start: 0.8181 (ptm) cc_final: 0.7787 (ptm) REVERT: N 26 ASP cc_start: 0.7641 (p0) cc_final: 0.7325 (p0) REVERT: N 38 GLN cc_start: 0.7975 (mt0) cc_final: 0.7715 (mt0) REVERT: N 84 ASP cc_start: 0.7791 (m-30) cc_final: 0.7446 (m-30) REVERT: N 201 GLU cc_start: 0.8040 (mp0) cc_final: 0.7584 (mp0) REVERT: e 122 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.3808 (pp-130) outliers start: 84 outliers final: 47 residues processed: 415 average time/residue: 0.5059 time to fit residues: 250.8064 Evaluate side-chains 402 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 342 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 187 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 300 optimal weight: 0.0970 chunk 235 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN K 88 ASN L -12 GLN N 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112304 restraints weight = 32908.682| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.25 r_work: 0.3258 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 24897 Z= 0.131 Angle : 0.578 17.041 33781 Z= 0.304 Chirality : 0.043 0.215 3924 Planarity : 0.004 0.074 4293 Dihedral : 4.058 25.598 3467 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.98 % Allowed : 21.99 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3140 helix: 2.33 (0.14), residues: 1252 sheet: -1.29 (0.19), residues: 690 loop : -1.41 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 88 TYR 0.041 0.001 TYR J 98 PHE 0.022 0.001 PHE H 200 TRP 0.040 0.002 TRP G 220 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00315 (24894) covalent geometry : angle 0.57495 (33775) SS BOND : bond 0.01846 ( 3) SS BOND : angle 4.60032 ( 6) hydrogen bonds : bond 0.03204 ( 1287) hydrogen bonds : angle 4.48558 ( 3666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 359 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 106 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 7 SER cc_start: 0.6138 (OUTLIER) cc_final: 0.5804 (p) REVERT: B 63 PHE cc_start: 0.6162 (m-80) cc_final: 0.5933 (m-80) REVERT: B 70 GLU cc_start: 0.8486 (tt0) cc_final: 0.8017 (tm-30) REVERT: B 135 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6840 (tt) REVERT: C 102 ASN cc_start: 0.8512 (t0) cc_final: 0.7930 (t0) REVERT: C 231 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 11 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7449 (p) REVERT: D 13 ASP cc_start: 0.7890 (t0) cc_final: 0.7577 (t0) REVERT: D 37 SER cc_start: 0.7428 (t) cc_final: 0.6405 (p) REVERT: D 67 GLU cc_start: 0.8651 (mp0) cc_final: 0.8370 (mp0) REVERT: D 98 MET cc_start: 0.7764 (mmt) cc_final: 0.7379 (mmm) REVERT: D 139 ASN cc_start: 0.8966 (t0) cc_final: 0.8710 (t0) REVERT: E 28 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5949 (mp) REVERT: E 236 ASP cc_start: 0.8309 (m-30) cc_final: 0.7861 (p0) REVERT: G 20 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7898 (ptm160) REVERT: G 38 LEU cc_start: 0.7564 (tt) cc_final: 0.7255 (tm) REVERT: G 73 ASN cc_start: 0.7858 (m-40) cc_final: 0.6988 (p0) REVERT: G 155 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: G 193 ILE cc_start: 0.7542 (mt) cc_final: 0.7330 (mp) REVERT: H 163 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: H 172 SER cc_start: 0.7558 (m) cc_final: 0.6850 (t) REVERT: H 201 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6398 (ppp) REVERT: H 241 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4351 (p90) REVERT: I 36 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6317 (t80) REVERT: I 64 GLU cc_start: 0.7263 (tp30) cc_final: 0.6967 (tp30) REVERT: J 48 ASN cc_start: 0.8245 (t0) cc_final: 0.7916 (t0) REVERT: J 162 MET cc_start: 0.7978 (mtm) cc_final: 0.7567 (mpt) REVERT: J 212 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7346 (mmmt) REVERT: K 178 TYR cc_start: 0.5143 (m-80) cc_final: 0.4842 (m-10) REVERT: L 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6884 (t160) REVERT: L 45 MET cc_start: 0.7859 (mtp) cc_final: 0.7501 (mtp) REVERT: L 102 SER cc_start: 0.8075 (t) cc_final: 0.7673 (m) REVERT: L 111 MET cc_start: 0.8269 (tpp) cc_final: 0.8039 (tpp) REVERT: M 110 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: M 142 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: M 146 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7137 (ttpp) REVERT: N 22 MET cc_start: 0.8281 (ptm) cc_final: 0.7788 (ptm) REVERT: N 26 ASP cc_start: 0.7623 (p0) cc_final: 0.7326 (p0) REVERT: N 38 GLN cc_start: 0.7986 (mt0) cc_final: 0.7716 (mt0) REVERT: N 201 GLU cc_start: 0.8090 (mp0) cc_final: 0.7619 (mp0) REVERT: e 122 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.3809 (pp-130) outliers start: 74 outliers final: 45 residues processed: 409 average time/residue: 0.4742 time to fit residues: 232.7517 Evaluate side-chains 405 residues out of total 2830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 TRP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 159 CYS Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 75 ARG Chi-restraints excluded: chain e residue 122 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 231 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN G 67 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** I -17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 85 GLN J 171 GLN L -12 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108930 restraints weight = 33698.757| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.14 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 24897 Z= 0.216 Angle : 0.642 16.665 33781 Z= 0.340 Chirality : 0.046 0.252 3924 Planarity : 0.004 0.070 4293 Dihedral : 4.305 28.112 3467 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 3.26 % Allowed : 21.83 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3140 helix: 2.08 (0.14), residues: 1248 sheet: -1.46 (0.18), residues: 695 loop : -1.49 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 88 TYR 0.047 0.002 TYR J 98 PHE 0.027 0.002 PHE N 37 TRP 0.046 0.002 TRP G 220 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00531 (24894) covalent geometry : angle 0.63884 (33775) SS BOND : bond 0.01917 ( 3) SS BOND : angle 4.97762 ( 6) hydrogen bonds : bond 0.03885 ( 1287) hydrogen bonds : angle 4.71068 ( 3666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6651.90 seconds wall clock time: 114 minutes 45.96 seconds (6885.96 seconds total)