Starting phenix.real_space_refine on Sun Aug 24 18:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qym_18758/08_2025/8qym_18758.map" } resolution = 2.73 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= 0.011 sd= 0.121 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 137 5.16 5 C 14146 2.51 5 N 3798 2.21 5 O 4154 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22235 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1790 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1962 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 243} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1866 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1778 Unusual residues: {'ACE': 1} Classifications: {'peptide': 232, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1886 Unusual residues: {'ACE': 1} Classifications: {'peptide': 239, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1868 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1883 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "I" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2082 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1929 Unusual residues: {'ACE': 1} Classifications: {'peptide': 248, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "K" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1589 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1396 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1347 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 2, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 4.57, per 1000 atoms: 0.21 Number of scatterers: 22235 At special positions: 0 Unit cell: (133.638, 142.15, 146.406, 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 137 16.00 O 4154 8.00 N 3798 7.00 C 14146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 936.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5350 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 28 sheets defined 40.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.768A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.852A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.732A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.549A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.186A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.667A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.627A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 229 through 250 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.699A pdb=" N GLN C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 25 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.594A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.670A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 4.021A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.758A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.557A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.908A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 221 through 238 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 31 through 34 removed outlier: 3.827A pdb=" N GLY D 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 104 Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.708A pdb=" N VAL D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 184 removed outlier: 3.995A pdb=" N ALA D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.557A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.934A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 77 through 99 removed outlier: 3.753A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.195A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 179 removed outlier: 4.117A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.678A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.655A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.868A pdb=" N SER F 34 " --> pdb=" O VAL F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.580A pdb=" N GLU F 184 " --> pdb=" O GLN F 181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 181 through 185' Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.433A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.527A pdb=" N LEU F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 3.509A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.715A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.692A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'H' and resid 46 through 54 removed outlier: 4.567A pdb=" N LEU H 50 " --> pdb=" O HIS H 46 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 71 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.699A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 108 through 111 removed outlier: 4.027A pdb=" N THR H 111 " --> pdb=" O ASN H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.568A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.670A pdb=" N LEU I 184 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 259 through 263 removed outlier: 4.262A pdb=" N VAL I 263 " --> pdb=" O LYS I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 278 Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.791A pdb=" N PHE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.806A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.703A pdb=" N GLU J 222 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.773A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.526A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 205 removed outlier: 3.733A pdb=" N GLY K 205 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 79 removed outlier: 3.584A pdb=" N LYS L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE L 69 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG L 70 " --> pdb=" O ARG L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 97 Processing helix chain 'L' and resid 142 through 154 removed outlier: 4.198A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 Processing helix chain 'M' and resid 52 through 72 removed outlier: 3.621A pdb=" N PHE M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 93 removed outlier: 3.557A pdb=" N ARG M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 152 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.687A pdb=" N ASN A 214 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.500A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.746A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.835A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.835A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 141 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 145 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.547A pdb=" N ILE E 72 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 138 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.613A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 226 " --> pdb=" O TRP F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.707A pdb=" N MET F 76 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 5 through 6 removed outlier: 6.186A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.198A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.637A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 56 through 57 removed outlier: 6.890A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AC1, first strand: chain 'J' and resid 1 through 4 removed outlier: 3.507A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.305A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.305A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 41 through 42 removed outlier: 6.402A pdb=" N ILE K 84 " --> pdb=" O ILE K 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 41 through 42 Processing sheet with id=AC6, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.704A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 256 through 261 removed outlier: 3.658A pdb=" N UNK K 256 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 42 through 44 Processing sheet with id=AC9, first strand: chain 'M' and resid 129 through 131 removed outlier: 5.064A pdb=" N VAL M 180 " --> pdb=" O LEU M 191 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.597A pdb=" N ILE M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3195 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: 3.63 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3689 1.30 - 1.42: 5595 1.42 - 1.55: 13145 1.55 - 1.68: 0 1.68 - 1.81: 212 Bond restraints: 22641 Sorted by residual: bond pdb=" N LEU D 3 " pdb=" CA LEU D 3 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.23e+00 bond pdb=" N PHE D 2 " pdb=" CA PHE D 2 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.29e-02 6.01e+03 4.09e+00 bond pdb=" N ARG E 3 " pdb=" CA ARG E 3 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.35e-02 5.49e+03 4.03e+00 bond pdb=" N PHE E 2 " pdb=" CA PHE E 2 " ideal model delta sigma weight residual 1.456 1.477 -0.022 1.26e-02 6.30e+03 2.96e+00 bond pdb=" C ACE J 0 " pdb=" N MET J 1 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 22636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 30387 2.29 - 4.57: 200 4.57 - 6.86: 14 6.86 - 9.15: 0 9.15 - 11.43: 1 Bond angle restraints: 30602 Sorted by residual: angle pdb=" CA PHE E 2 " pdb=" CB PHE E 2 " pdb=" CG PHE E 2 " ideal model delta sigma weight residual 113.80 118.33 -4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C ACE J 0 " pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 121.70 110.27 11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N ARG E 3 " pdb=" CA ARG E 3 " pdb=" C ARG E 3 " ideal model delta sigma weight residual 113.38 109.55 3.83 1.23e+00 6.61e-01 9.70e+00 angle pdb=" N PHE E 2 " pdb=" CA PHE E 2 " pdb=" C PHE E 2 " ideal model delta sigma weight residual 112.92 109.30 3.62 1.23e+00 6.61e-01 8.69e+00 angle pdb=" CA PHE D 2 " pdb=" C PHE D 2 " pdb=" O PHE D 2 " ideal model delta sigma weight residual 121.44 118.09 3.35 1.17e+00 7.31e-01 8.22e+00 ... (remaining 30597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 12507 17.69 - 35.38: 997 35.38 - 53.08: 152 53.08 - 70.77: 52 70.77 - 88.46: 18 Dihedral angle restraints: 13726 sinusoidal: 5419 harmonic: 8307 Sorted by residual: dihedral pdb=" CH3 ACE J 0 " pdb=" C ACE J 0 " pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -128.99 -51.01 1 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLY L 101 " pdb=" CA GLY L 101 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU L 97 " pdb=" C GLU L 97 " pdb=" N LYS L 98 " pdb=" CA LYS L 98 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 13723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2320 0.033 - 0.067: 787 0.067 - 0.100: 224 0.100 - 0.134: 149 0.134 - 0.167: 4 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CA VAL D 184 " pdb=" N VAL D 184 " pdb=" C VAL D 184 " pdb=" CB VAL D 184 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA VAL A 75 " pdb=" N VAL A 75 " pdb=" C VAL A 75 " pdb=" CB VAL A 75 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA THR M 96 " pdb=" N THR M 96 " pdb=" C THR M 96 " pdb=" CB THR M 96 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 3481 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.100 2.00e-02 2.50e+03 2.79e-01 9.70e+02 pdb=" O ACE J 0 " 0.029 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.233 2.00e-02 2.50e+03 pdb=" N MET J 1 " 0.450 2.00e-02 2.50e+03 pdb=" CA MET J 1 " -0.346 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE E 0 " 0.018 2.00e-02 2.50e+03 6.27e-02 4.92e+01 pdb=" O ACE E 0 " 0.010 2.00e-02 2.50e+03 pdb=" CH3 ACE E 0 " -0.057 2.00e-02 2.50e+03 pdb=" N MET E 1 " 0.102 2.00e-02 2.50e+03 pdb=" CA MET E 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " -0.010 2.00e-02 2.50e+03 3.37e-02 1.42e+01 pdb=" O ACE D 0 " -0.005 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " 0.030 2.00e-02 2.50e+03 pdb=" N MET D 1 " -0.055 2.00e-02 2.50e+03 pdb=" CA MET D 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2447 2.75 - 3.29: 19567 3.29 - 3.83: 33973 3.83 - 4.36: 40120 4.36 - 4.90: 74624 Nonbonded interactions: 170731 Sorted by model distance: nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 163 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLN C 146 " pdb=" ND2 ASN C 159 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR E 207 " pdb=" O ASP E 226 " model vdw 2.232 3.040 nonbonded pdb=" O PHE J 15 " pdb=" OG1 THR J 16 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR K 44 " pdb=" NZ LYS K 76 " model vdw 2.257 3.120 ... (remaining 170726 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: 1.730 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 18.880 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.002 0.047 22641 Z= 0.108 Angle : 0.470 11.434 30602 Z= 0.253 Chirality : 0.042 0.167 3484 Planarity : 0.006 0.279 3909 Dihedral : 13.613 88.462 8376 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.18 (0.16), residues: 2802 helix: 2.60 (0.17), residues: 1024 sheet: 0.63 (0.21), residues: 628 loop : -0.83 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 86 TYR 0.013 0.001 TYR A 83 PHE 0.019 0.001 PHE L 69 TRP 0.050 0.001 TRP F 216 HIS 0.004 0.001 HIS M 99 Details of bonding type rmsd covalent geometry : bond 0.00232 (22641) covalent geometry : angle 0.47011 (30602) hydrogen bonds : bond 0.17555 ( 1112) hydrogen bonds : angle 5.85042 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.7802 (t70) cc_final: 0.7585 (t0) REVERT: G 147 GLN cc_start: 0.8497 (mt0) cc_final: 0.8213 (tt0) REVERT: I 199 ASP cc_start: 0.8310 (m-30) cc_final: 0.7996 (m-30) REVERT: K 31 LYS cc_start: 0.7705 (tmmt) cc_final: 0.7460 (tppt) REVERT: L 142 CYS cc_start: 0.8044 (m) cc_final: 0.7740 (m) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.7199 time to fit residues: 235.0901 Evaluate side-chains 240 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 ASN E 203 GLN F 181 GLN G 147 GLN H 90 GLN I 40 GLN I 53 GLN J 89 GLN L 169 GLN L 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079761 restraints weight = 36033.945| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.36 r_work: 0.2894 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22641 Z= 0.187 Angle : 0.564 8.744 30602 Z= 0.302 Chirality : 0.045 0.165 3484 Planarity : 0.005 0.058 3909 Dihedral : 4.183 41.852 3105 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.01 % Allowed : 7.55 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.05 (0.16), residues: 2802 helix: 2.43 (0.16), residues: 1045 sheet: 0.73 (0.21), residues: 613 loop : -1.00 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 38 TYR 0.019 0.002 TYR B 136 PHE 0.026 0.001 PHE L 69 TRP 0.029 0.002 TRP F 216 HIS 0.005 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00466 (22641) covalent geometry : angle 0.56393 (30602) hydrogen bonds : bond 0.06035 ( 1112) hydrogen bonds : angle 4.40235 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.706 Fit side-chains REVERT: B 100 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 178 ASP cc_start: 0.8463 (t70) cc_final: 0.8095 (t0) REVERT: B 235 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7689 (tp-100) REVERT: D 168 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7802 (tpp80) REVERT: E 174 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7851 (tpt-90) REVERT: F 144 ASN cc_start: 0.8241 (p0) cc_final: 0.7967 (p0) REVERT: I 199 ASP cc_start: 0.8310 (m-30) cc_final: 0.7930 (m-30) REVERT: J 50 ASP cc_start: 0.9119 (p0) cc_final: 0.8518 (p0) REVERT: K 31 LYS cc_start: 0.7845 (tmmt) cc_final: 0.7506 (tppt) REVERT: L 142 CYS cc_start: 0.8224 (m) cc_final: 0.7843 (m) REVERT: M 65 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7815 (tm-30) outliers start: 24 outliers final: 7 residues processed: 256 average time/residue: 0.7076 time to fit residues: 201.5899 Evaluate side-chains 245 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain E residue 174 ARG Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 231 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 181 GLN H 88 GLN I 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073144 restraints weight = 33351.580| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.38 r_work: 0.2750 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22641 Z= 0.132 Angle : 0.498 8.529 30602 Z= 0.269 Chirality : 0.043 0.147 3484 Planarity : 0.005 0.057 3909 Dihedral : 4.066 40.189 3105 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.22 % Allowed : 9.81 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.19 (0.16), residues: 2802 helix: 2.53 (0.16), residues: 1043 sheet: 0.83 (0.20), residues: 624 loop : -0.95 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 38 TYR 0.016 0.001 TYR E 123 PHE 0.024 0.001 PHE L 69 TRP 0.016 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00317 (22641) covalent geometry : angle 0.49822 (30602) hydrogen bonds : bond 0.04888 ( 1112) hydrogen bonds : angle 4.12467 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.663 Fit side-chains REVERT: B 52 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 178 ASP cc_start: 0.8299 (t70) cc_final: 0.7911 (t0) REVERT: D 168 ARG cc_start: 0.8189 (tpt-90) cc_final: 0.7768 (tpp80) REVERT: H 110 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: I 199 ASP cc_start: 0.8328 (m-30) cc_final: 0.7932 (m-30) REVERT: K 31 LYS cc_start: 0.7687 (tmmt) cc_final: 0.7353 (tppt) REVERT: L 81 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: L 142 CYS cc_start: 0.8191 (m) cc_final: 0.7572 (m) REVERT: L 144 GLU cc_start: 0.8058 (pm20) cc_final: 0.7735 (pm20) REVERT: L 145 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: M 65 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7665 (tm-30) outliers start: 29 outliers final: 12 residues processed: 254 average time/residue: 0.7029 time to fit residues: 198.5778 Evaluate side-chains 251 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 145 GLN Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 246 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 91 optimal weight: 0.0070 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 186 HIS D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.069525 restraints weight = 33422.835| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.37 r_work: 0.2685 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 22641 Z= 0.269 Angle : 0.629 9.875 30602 Z= 0.335 Chirality : 0.048 0.183 3484 Planarity : 0.006 0.066 3909 Dihedral : 4.502 44.897 3105 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.80 % Allowed : 11.24 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 0.77 (0.15), residues: 2802 helix: 2.19 (0.16), residues: 1040 sheet: 0.74 (0.20), residues: 610 loop : -1.24 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 38 TYR 0.024 0.002 TYR E 123 PHE 0.029 0.002 PHE L 69 TRP 0.015 0.002 TRP D 100 HIS 0.007 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00689 (22641) covalent geometry : angle 0.62923 (30602) hydrogen bonds : bond 0.07209 ( 1112) hydrogen bonds : angle 4.36919 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.859 Fit side-chains REVERT: B 178 ASP cc_start: 0.8542 (t70) cc_final: 0.8093 (t0) REVERT: B 235 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7623 (tp-100) REVERT: E 174 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7998 (tpt-90) REVERT: G 145 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8039 (pm20) REVERT: H 110 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: I 199 ASP cc_start: 0.8379 (m-30) cc_final: 0.8016 (m-30) REVERT: J 50 ASP cc_start: 0.9107 (p0) cc_final: 0.8515 (p0) REVERT: J 180 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7983 (mtt-85) REVERT: K 31 LYS cc_start: 0.7841 (tmmt) cc_final: 0.7458 (tptm) REVERT: L 144 GLU cc_start: 0.8110 (pm20) cc_final: 0.7739 (pm20) REVERT: L 145 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: M 65 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: M 134 TYR cc_start: 0.5179 (OUTLIER) cc_final: 0.4959 (p90) outliers start: 43 outliers final: 22 residues processed: 255 average time/residue: 0.7446 time to fit residues: 210.9046 Evaluate side-chains 253 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 174 ARG Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 145 GLN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 134 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 161 ARG Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 275 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN F 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074751 restraints weight = 33007.525| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.37 r_work: 0.2783 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22641 Z= 0.097 Angle : 0.470 8.815 30602 Z= 0.254 Chirality : 0.041 0.146 3484 Planarity : 0.005 0.053 3909 Dihedral : 4.010 40.329 3105 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.34 % Allowed : 12.62 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.15 (0.16), residues: 2802 helix: 2.52 (0.16), residues: 1044 sheet: 0.77 (0.20), residues: 630 loop : -0.97 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 38 TYR 0.026 0.001 TYR E 123 PHE 0.019 0.001 PHE L 69 TRP 0.018 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00208 (22641) covalent geometry : angle 0.47002 (30602) hydrogen bonds : bond 0.03778 ( 1112) hydrogen bonds : angle 3.93939 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.971 Fit side-chains REVERT: B 178 ASP cc_start: 0.8195 (t70) cc_final: 0.7753 (t0) REVERT: B 235 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7579 (tp-100) REVERT: H 110 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: I 199 ASP cc_start: 0.8320 (m-30) cc_final: 0.7966 (m-30) REVERT: J 180 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7999 (mtt-85) REVERT: K 31 LYS cc_start: 0.7777 (tmmt) cc_final: 0.7439 (tptm) REVERT: M 65 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7473 (tm-30) outliers start: 32 outliers final: 12 residues processed: 246 average time/residue: 0.8213 time to fit residues: 224.6506 Evaluate side-chains 243 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 59 optimal weight: 0.0170 chunk 67 optimal weight: 0.4980 chunk 229 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN F 181 GLN I 40 GLN M 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.073994 restraints weight = 33200.683| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.36 r_work: 0.2766 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22641 Z= 0.111 Angle : 0.478 8.310 30602 Z= 0.257 Chirality : 0.042 0.143 3484 Planarity : 0.004 0.054 3909 Dihedral : 3.948 39.110 3105 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.13 % Allowed : 13.38 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.24 (0.16), residues: 2802 helix: 2.61 (0.16), residues: 1044 sheet: 0.83 (0.20), residues: 635 loop : -0.96 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.028 0.001 TYR E 123 PHE 0.024 0.001 PHE L 69 TRP 0.017 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00259 (22641) covalent geometry : angle 0.47789 (30602) hydrogen bonds : bond 0.04246 ( 1112) hydrogen bonds : angle 3.89610 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.856 Fit side-chains REVERT: A 150 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8600 (t0) REVERT: B 178 ASP cc_start: 0.8218 (t70) cc_final: 0.7840 (t0) REVERT: D 100 TRP cc_start: 0.7950 (t60) cc_final: 0.7677 (t60) REVERT: H 110 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: I 199 ASP cc_start: 0.8337 (m-30) cc_final: 0.7961 (m-30) REVERT: K 31 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7474 (tptm) REVERT: M 65 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7506 (tm-30) outliers start: 27 outliers final: 15 residues processed: 253 average time/residue: 0.7461 time to fit residues: 210.1022 Evaluate side-chains 250 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 274 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN G 147 GLN I 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.070678 restraints weight = 33223.194| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.37 r_work: 0.2710 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 22641 Z= 0.206 Angle : 0.577 9.168 30602 Z= 0.308 Chirality : 0.045 0.165 3484 Planarity : 0.005 0.062 3909 Dihedral : 4.292 45.180 3105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.43 % Allowed : 13.58 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 0.98 (0.16), residues: 2802 helix: 2.38 (0.16), residues: 1044 sheet: 0.79 (0.20), residues: 617 loop : -1.13 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.033 0.002 TYR E 123 PHE 0.027 0.002 PHE L 69 TRP 0.016 0.002 TRP D 100 HIS 0.006 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00521 (22641) covalent geometry : angle 0.57701 (30602) hydrogen bonds : bond 0.06122 ( 1112) hydrogen bonds : angle 4.15817 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.997 Fit side-chains REVERT: A 150 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8712 (t0) REVERT: A 163 MET cc_start: 0.9253 (ptt) cc_final: 0.9038 (ptt) REVERT: B 178 ASP cc_start: 0.8420 (t70) cc_final: 0.7964 (t0) REVERT: F 82 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7591 (mp) REVERT: H 110 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: I 199 ASP cc_start: 0.8357 (m-30) cc_final: 0.7999 (m-30) REVERT: J 50 ASP cc_start: 0.9079 (p0) cc_final: 0.8485 (p0) REVERT: K 31 LYS cc_start: 0.7862 (tmmt) cc_final: 0.7498 (tptm) REVERT: M 65 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7829 (tm-30) outliers start: 34 outliers final: 18 residues processed: 253 average time/residue: 0.6938 time to fit residues: 195.5194 Evaluate side-chains 252 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 279 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 222 optimal weight: 0.0050 chunk 240 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN G 147 GLN I 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071940 restraints weight = 33002.875| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.36 r_work: 0.2730 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22641 Z= 0.157 Angle : 0.533 8.603 30602 Z= 0.286 Chirality : 0.044 0.149 3484 Planarity : 0.005 0.063 3909 Dihedral : 4.226 46.866 3105 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.34 % Allowed : 14.05 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 1.02 (0.16), residues: 2802 helix: 2.42 (0.16), residues: 1043 sheet: 0.77 (0.20), residues: 624 loop : -1.10 (0.16), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.035 0.001 TYR E 123 PHE 0.026 0.001 PHE L 69 TRP 0.026 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00388 (22641) covalent geometry : angle 0.53294 (30602) hydrogen bonds : bond 0.05230 ( 1112) hydrogen bonds : angle 4.07017 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.663 Fit side-chains REVERT: A 150 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8695 (t0) REVERT: B 178 ASP cc_start: 0.8335 (t70) cc_final: 0.7870 (t0) REVERT: D 71 ASP cc_start: 0.8395 (t70) cc_final: 0.8128 (t0) REVERT: F 82 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (mp) REVERT: H 110 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: I 199 ASP cc_start: 0.8362 (m-30) cc_final: 0.8005 (m-30) REVERT: K 31 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7504 (tptm) REVERT: M 65 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: M 134 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4948 (p90) outliers start: 32 outliers final: 18 residues processed: 254 average time/residue: 0.7178 time to fit residues: 203.1723 Evaluate side-chains 256 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 134 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 253 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN G 147 GLN I 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.070902 restraints weight = 33217.055| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.37 r_work: 0.2712 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22641 Z= 0.195 Angle : 0.571 8.971 30602 Z= 0.306 Chirality : 0.045 0.162 3484 Planarity : 0.005 0.066 3909 Dihedral : 4.355 50.431 3105 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.34 % Allowed : 14.26 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 0.89 (0.16), residues: 2802 helix: 2.32 (0.16), residues: 1044 sheet: 0.74 (0.20), residues: 617 loop : -1.19 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 38 TYR 0.037 0.002 TYR E 123 PHE 0.027 0.001 PHE L 69 TRP 0.031 0.002 TRP D 100 HIS 0.006 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00493 (22641) covalent geometry : angle 0.57134 (30602) hydrogen bonds : bond 0.05949 ( 1112) hydrogen bonds : angle 4.15198 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.812 Fit side-chains REVERT: A 150 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8706 (t0) REVERT: B 178 ASP cc_start: 0.8430 (t70) cc_final: 0.7934 (t0) REVERT: D 71 ASP cc_start: 0.8431 (t70) cc_final: 0.8152 (t0) REVERT: F 82 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7594 (mp) REVERT: H 110 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: I 199 ASP cc_start: 0.8368 (m-30) cc_final: 0.8013 (m-30) REVERT: K 31 LYS cc_start: 0.7890 (tmmt) cc_final: 0.7524 (tptm) REVERT: M 65 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: M 98 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: M 134 TYR cc_start: 0.5168 (OUTLIER) cc_final: 0.4952 (p90) outliers start: 32 outliers final: 20 residues processed: 250 average time/residue: 0.7061 time to fit residues: 196.8948 Evaluate side-chains 257 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 134 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 3 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 74 optimal weight: 8.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN G 147 GLN I 53 GLN L 162 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.071532 restraints weight = 33243.761| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.31 r_work: 0.2753 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22641 Z= 0.178 Angle : 0.558 8.606 30602 Z= 0.299 Chirality : 0.044 0.159 3484 Planarity : 0.005 0.065 3909 Dihedral : 4.323 50.087 3105 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.30 % Allowed : 14.55 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 0.93 (0.16), residues: 2802 helix: 2.34 (0.16), residues: 1044 sheet: 0.73 (0.20), residues: 624 loop : -1.16 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 38 TYR 0.038 0.001 TYR E 123 PHE 0.028 0.001 PHE L 69 TRP 0.033 0.002 TRP D 100 HIS 0.006 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00446 (22641) covalent geometry : angle 0.55767 (30602) hydrogen bonds : bond 0.05630 ( 1112) hydrogen bonds : angle 4.11958 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.754 Fit side-chains REVERT: A 150 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8685 (t0) REVERT: B 178 ASP cc_start: 0.8391 (t70) cc_final: 0.7884 (t0) REVERT: D 71 ASP cc_start: 0.8441 (t70) cc_final: 0.8166 (t0) REVERT: F 82 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7558 (mp) REVERT: H 110 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: I 199 ASP cc_start: 0.8384 (m-30) cc_final: 0.8034 (m-30) REVERT: J 180 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8012 (mtt-85) REVERT: K 31 LYS cc_start: 0.7871 (tmmt) cc_final: 0.7507 (tptm) REVERT: M 65 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: M 98 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: M 134 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4922 (p90) outliers start: 31 outliers final: 20 residues processed: 250 average time/residue: 0.6695 time to fit residues: 185.8536 Evaluate side-chains 260 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 134 TYR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 70 optimal weight: 2.9990 chunk 201 optimal weight: 0.0270 chunk 248 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN F 144 ASN G 147 GLN L 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.071529 restraints weight = 32931.965| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.36 r_work: 0.2724 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 22641 Z= 0.203 Angle : 0.773 59.200 30602 Z= 0.432 Chirality : 0.044 0.499 3484 Planarity : 0.006 0.250 3909 Dihedral : 4.320 49.894 3105 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.22 % Allowed : 14.59 % Favored : 84.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.92 % 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 aren not related in a simple way. whole: 0.94 (0.16), residues: 2802 helix: 2.37 (0.16), residues: 1044 sheet: 0.73 (0.20), residues: 619 loop : -1.17 (0.16), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.032 0.001 TYR E 123 PHE 0.028 0.001 PHE L 69 TRP 0.029 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00420 (22641) covalent geometry : angle 0.77325 (30602) hydrogen bonds : bond 0.05373 ( 1112) hydrogen bonds : angle 4.11697 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7795.00 seconds wall clock time: 133 minutes 7.95 seconds (7987.95 seconds total)