Starting phenix.real_space_refine on Thu Jun 19 02:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qym_18758/06_2025/8qym_18758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qym_18758/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qym_18758/06_2025/8qym_18758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qym_18758/06_2025/8qym_18758.map" model { file = "/net/cci-nas-00/data/ceres_data/8qym_18758/06_2025/8qym_18758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qym_18758/06_2025/8qym_18758.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 13.07, per 1000 atoms: 0.59 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: 5.20 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.20 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: 6.60 Time building geometry restraints manager: 6.15 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: 14.490 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: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 47.950 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.050 0.001 TRP F 216 HIS 0.004 0.001 HIS M 99 PHE 0.019 0.001 PHE L 69 TYR 0.013 0.001 TYR A 83 ARG 0.004 0.000 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.17555 ( 1112) hydrogen bonds : angle 5.85042 ( 3195) covalent geometry : bond 0.00232 (22641) covalent geometry : angle 0.47011 (30602) *********************** 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 : 2.577 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: 0.7748 (m) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 1.6497 time to fit residues: 541.3389 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 : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 0.0020 chunk 163 optimal weight: 3.9990 chunk 254 optimal weight: 0.2980 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 118 ASN E 203 GLN G 147 GLN H 90 GLN I 40 GLN J 89 GLN L 169 GLN L 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082392 restraints weight = 35774.737| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.36 r_work: 0.2965 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0891 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= 0.116 Angle : 0.496 8.064 30602 Z= 0.267 Chirality : 0.042 0.149 3484 Planarity : 0.004 0.056 3909 Dihedral : 3.903 39.190 3105 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.96 % Allowed : 6.62 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2802 helix: 2.60 (0.16), residues: 1046 sheet: 0.83 (0.21), residues: 618 loop : -0.84 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 216 HIS 0.004 0.001 HIS M 99 PHE 0.022 0.001 PHE L 69 TYR 0.015 0.001 TYR A 83 ARG 0.008 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1112) hydrogen bonds : angle 4.29678 ( 3195) covalent geometry : bond 0.00263 (22641) covalent geometry : angle 0.49551 (30602) *********************** 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 269 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 5.298 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.8288 (t70) cc_final: 0.7898 (t0) REVERT: B 235 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7660 (tp-100) REVERT: D 100 TRP cc_start: 0.8009 (t60) cc_final: 0.7789 (t60) REVERT: D 168 ARG cc_start: 0.8147 (tpt-90) cc_final: 0.7768 (tpp80) REVERT: I 199 ASP cc_start: 0.8266 (m-30) cc_final: 0.7869 (m-30) REVERT: K 31 LYS cc_start: 0.7760 (tmmt) cc_final: 0.7435 (tppt) REVERT: L 142 CYS cc_start: 0.8176 (m) cc_final: 0.7778 (m) REVERT: M 65 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: M 90 ASP cc_start: 0.8337 (t0) cc_final: 0.7949 (m-30) outliers start: 23 outliers final: 9 residues processed: 257 average time/residue: 2.1737 time to fit residues: 626.0976 Evaluate side-chains 248 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 SER Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain L residue 153 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 89 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN D 186 HIS F 181 GLN H 88 GLN I 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069939 restraints weight = 33076.346| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.37 r_work: 0.2694 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22641 Z= 0.263 Angle : 0.623 9.747 30602 Z= 0.332 Chirality : 0.048 0.186 3484 Planarity : 0.005 0.062 3909 Dihedral : 4.415 42.406 3105 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.38 % Allowed : 9.39 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2802 helix: 2.27 (0.16), residues: 1043 sheet: 0.80 (0.20), residues: 611 loop : -1.14 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.028 0.002 PHE L 69 TYR 0.020 0.002 TYR B 136 ARG 0.007 0.001 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.07137 ( 1112) hydrogen bonds : angle 4.40208 ( 3195) covalent geometry : bond 0.00673 (22641) covalent geometry : angle 0.62272 (30602) *********************** 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 272 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 2.851 Fit side-chains REVERT: B 100 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: B 178 ASP cc_start: 0.8523 (t70) cc_final: 0.8103 (t0) REVERT: E 174 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7985 (tpt-90) REVERT: F 144 ASN cc_start: 0.8228 (p0) cc_final: 0.7929 (p0) REVERT: G 145 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8053 (pm20) REVERT: H 110 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: I 199 ASP cc_start: 0.8362 (m-30) cc_final: 0.8001 (m-30) REVERT: I 243 ASP cc_start: 0.8316 (t70) cc_final: 0.7902 (t0) REVERT: J 50 ASP cc_start: 0.9096 (p0) cc_final: 0.8492 (p0) REVERT: J 180 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7981 (mtt-85) REVERT: K 31 LYS cc_start: 0.7877 (tmmt) cc_final: 0.7523 (tppt) REVERT: L 144 GLU cc_start: 0.8040 (pm20) cc_final: 0.7716 (pm20) REVERT: L 145 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: M 65 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: M 134 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.4886 (p90) outliers start: 33 outliers final: 15 residues processed: 254 average time/residue: 1.8969 time to fit residues: 538.7545 Evaluate side-chains 249 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 43 VAL 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 62 MET Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 55 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 138 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN I 40 GLN I 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.074054 restraints weight = 33146.877| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.39 r_work: 0.2768 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 22641 Z= 0.101 Angle : 0.475 8.748 30602 Z= 0.258 Chirality : 0.042 0.145 3484 Planarity : 0.005 0.053 3909 Dihedral : 4.042 39.198 3105 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.13 % Allowed : 11.19 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2802 helix: 2.55 (0.16), residues: 1044 sheet: 0.83 (0.20), residues: 625 loop : -0.96 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.020 0.001 PHE L 69 TYR 0.014 0.001 TYR K 51 ARG 0.008 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1112) hydrogen bonds : angle 4.04470 ( 3195) covalent geometry : bond 0.00224 (22641) covalent geometry : angle 0.47539 (30602) *********************** 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 261 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 2.546 Fit side-chains REVERT: B 52 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7986 (pp) REVERT: B 178 ASP cc_start: 0.8267 (t70) cc_final: 0.7815 (t0) REVERT: B 235 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7656 (tp-100) REVERT: G 145 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8081 (pm20) REVERT: I 199 ASP cc_start: 0.8346 (m-30) cc_final: 0.7941 (m-30) REVERT: I 243 ASP cc_start: 0.8251 (t70) cc_final: 0.7868 (t0) REVERT: J 180 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7982 (mtt-85) REVERT: K 31 LYS cc_start: 0.7779 (tmmt) cc_final: 0.7436 (tptm) REVERT: L 144 GLU cc_start: 0.8131 (pm20) cc_final: 0.7777 (pm20) REVERT: L 145 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: M 65 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7534 (tm-30) outliers start: 27 outliers final: 10 residues processed: 246 average time/residue: 1.6822 time to fit residues: 462.9336 Evaluate side-chains 240 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 174 MET 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 96 SER 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 65 GLN Chi-restraints excluded: chain M residue 141 SER 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 18 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN D 214 ASN F 181 GLN M 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071081 restraints weight = 33271.460| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.39 r_work: 0.2714 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22641 Z= 0.196 Angle : 0.555 8.704 30602 Z= 0.298 Chirality : 0.045 0.168 3484 Planarity : 0.005 0.062 3909 Dihedral : 4.234 39.659 3105 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.43 % Allowed : 12.29 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 2802 helix: 2.42 (0.16), residues: 1043 sheet: 0.83 (0.20), residues: 614 loop : -1.09 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 100 HIS 0.006 0.001 HIS I 125 PHE 0.027 0.001 PHE L 69 TYR 0.019 0.002 TYR K 51 ARG 0.008 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.05923 ( 1112) hydrogen bonds : angle 4.15008 ( 3195) covalent geometry : bond 0.00492 (22641) covalent geometry : angle 0.55530 (30602) *********************** 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 264 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 2.511 Fit side-chains REVERT: B 178 ASP cc_start: 0.8396 (t70) cc_final: 0.7951 (t0) REVERT: B 235 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7609 (tp-100) REVERT: F 82 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7593 (mp) REVERT: G 145 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8051 (pm20) REVERT: H 110 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: I 199 ASP cc_start: 0.8353 (m-30) cc_final: 0.7981 (m-30) REVERT: I 243 ASP cc_start: 0.8288 (t70) cc_final: 0.7899 (t0) REVERT: J 50 ASP cc_start: 0.9069 (p0) cc_final: 0.8499 (p0) REVERT: J 180 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7980 (mtt-85) REVERT: K 31 LYS cc_start: 0.7824 (tmmt) cc_final: 0.7464 (tptm) REVERT: L 144 GLU cc_start: 0.8186 (pm20) cc_final: 0.7823 (pm20) REVERT: L 145 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: M 65 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7782 (tm-30) outliers start: 34 outliers final: 20 residues processed: 249 average time/residue: 1.6246 time to fit residues: 453.7578 Evaluate side-chains 251 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 217 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 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 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 18 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 0.0170 chunk 184 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 109 GLN B 146 GLN D 214 ASN F 144 ASN F 181 GLN I 53 GLN M 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076070 restraints weight = 33062.387| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.37 r_work: 0.2805 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1316 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= 0.088 Angle : 0.451 9.480 30602 Z= 0.242 Chirality : 0.041 0.144 3484 Planarity : 0.004 0.050 3909 Dihedral : 3.832 33.280 3105 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.17 % Allowed : 12.62 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2802 helix: 2.68 (0.16), residues: 1045 sheet: 0.83 (0.20), residues: 642 loop : -0.88 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.019 0.001 PHE K 79 TYR 0.013 0.001 TYR K 51 ARG 0.010 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1112) hydrogen bonds : angle 3.81948 ( 3195) covalent geometry : bond 0.00191 (22641) covalent geometry : angle 0.45120 (30602) *********************** 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 267 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 2.920 Fit side-chains REVERT: B 178 ASP cc_start: 0.8108 (t70) cc_final: 0.7668 (t0) REVERT: B 235 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7609 (tp-100) REVERT: D 100 TRP cc_start: 0.7927 (t60) cc_final: 0.7678 (t60) REVERT: G 145 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8073 (pm20) REVERT: H 110 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: I 199 ASP cc_start: 0.8319 (m-30) cc_final: 0.7929 (m-30) REVERT: J 55 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8409 (ppp) REVERT: K 31 LYS cc_start: 0.7780 (tmmt) cc_final: 0.7458 (tptm) REVERT: M 65 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7496 (tm-30) outliers start: 28 outliers final: 11 residues processed: 253 average time/residue: 1.6549 time to fit residues: 469.7902 Evaluate side-chains 241 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 181 ASP 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 L residue 115 LYS 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 126 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 184 optimal weight: 0.0870 chunk 204 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 overall best weight: 3.5564 ------------------------------------------------------------------------------- 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 I 53 GLN M 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071046 restraints weight = 33255.758| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.37 r_work: 0.2718 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22641 Z= 0.206 Angle : 0.566 8.742 30602 Z= 0.303 Chirality : 0.045 0.165 3484 Planarity : 0.005 0.060 3909 Dihedral : 4.204 41.303 3105 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.13 % Allowed : 13.33 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2802 helix: 2.46 (0.16), residues: 1044 sheet: 0.89 (0.20), residues: 613 loop : -1.08 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 100 HIS 0.006 0.001 HIS I 125 PHE 0.027 0.002 PHE L 69 TYR 0.020 0.002 TYR K 51 ARG 0.008 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 1112) hydrogen bonds : angle 4.11383 ( 3195) covalent geometry : bond 0.00521 (22641) covalent geometry : angle 0.56601 (30602) *********************** 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 259 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 2.538 Fit side-chains REVERT: A 150 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8682 (t0) REVERT: A 163 MET cc_start: 0.9255 (ptt) cc_final: 0.9020 (ptt) REVERT: B 178 ASP cc_start: 0.8411 (t70) cc_final: 0.7954 (t0) REVERT: F 82 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7567 (mp) REVERT: G 145 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8042 (pm20) REVERT: H 110 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: I 199 ASP cc_start: 0.8333 (m-30) cc_final: 0.7986 (m-30) REVERT: I 243 ASP cc_start: 0.8359 (t70) cc_final: 0.7955 (t0) REVERT: K 31 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7500 (tptm) REVERT: L 147 TYR cc_start: 0.7530 (t80) cc_final: 0.7321 (t80) REVERT: M 65 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: M 134 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4958 (p90) outliers start: 27 outliers final: 17 residues processed: 248 average time/residue: 1.6664 time to fit residues: 463.6706 Evaluate side-chains 253 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 I 53 GLN M 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074140 restraints weight = 33028.379| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.37 r_work: 0.2772 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22641 Z= 0.108 Angle : 0.485 8.212 30602 Z= 0.261 Chirality : 0.042 0.143 3484 Planarity : 0.005 0.053 3909 Dihedral : 3.981 40.505 3105 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.09 % Allowed : 13.79 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2802 helix: 2.61 (0.16), residues: 1044 sheet: 0.89 (0.20), residues: 623 loop : -0.98 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.022 0.001 PHE L 69 TYR 0.017 0.001 TYR D 185 ARG 0.009 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1112) hydrogen bonds : angle 3.91524 ( 3195) covalent geometry : bond 0.00248 (22641) covalent geometry : angle 0.48523 (30602) *********************** 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 255 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 3.362 Fit side-chains REVERT: A 150 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8594 (t0) REVERT: B 178 ASP cc_start: 0.8175 (t70) cc_final: 0.7755 (t0) REVERT: D 100 TRP cc_start: 0.7926 (t60) cc_final: 0.7669 (t60) REVERT: G 145 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8057 (pm20) REVERT: H 110 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: I 199 ASP cc_start: 0.8330 (m-30) cc_final: 0.7965 (m-30) REVERT: I 243 ASP cc_start: 0.8287 (t70) cc_final: 0.7873 (t0) REVERT: K 31 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7480 (tptm) REVERT: L 147 TYR cc_start: 0.7523 (t80) cc_final: 0.7315 (t80) REVERT: M 65 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7682 (tm-30) outliers start: 26 outliers final: 15 residues processed: 243 average time/residue: 1.6931 time to fit residues: 461.0635 Evaluate side-chains 244 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 96 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 214 ASN F 144 ASN I 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074191 restraints weight = 33126.945| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.37 r_work: 0.2773 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22641 Z= 0.110 Angle : 0.485 7.822 30602 Z= 0.261 Chirality : 0.042 0.143 3484 Planarity : 0.005 0.052 3909 Dihedral : 3.929 41.978 3105 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 14.26 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2802 helix: 2.66 (0.16), residues: 1044 sheet: 0.92 (0.20), residues: 623 loop : -0.96 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.023 0.001 PHE L 69 TYR 0.016 0.001 TYR K 51 ARG 0.011 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1112) hydrogen bonds : angle 3.87122 ( 3195) covalent geometry : bond 0.00255 (22641) covalent geometry : angle 0.48506 (30602) *********************** 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 254 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 3.821 Fit side-chains REVERT: A 150 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8609 (t0) REVERT: B 178 ASP cc_start: 0.8220 (t70) cc_final: 0.7839 (t0) REVERT: D 100 TRP cc_start: 0.7858 (t60) cc_final: 0.7635 (t60) REVERT: G 145 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8050 (pm20) REVERT: I 53 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: I 199 ASP cc_start: 0.8317 (m-30) cc_final: 0.7950 (m-30) REVERT: I 243 ASP cc_start: 0.8265 (t70) cc_final: 0.7861 (t0) REVERT: J 131 ASP cc_start: 0.8835 (m-30) cc_final: 0.8541 (m-30) REVERT: K 31 LYS cc_start: 0.7804 (tmmt) cc_final: 0.7481 (tptm) REVERT: L 192 LYS cc_start: 0.8396 (tttt) cc_final: 0.8126 (tptm) REVERT: M 65 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7519 (tm-30) outliers start: 24 outliers final: 15 residues processed: 245 average time/residue: 1.6976 time to fit residues: 467.2153 Evaluate side-chains 252 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 133 optimal weight: 0.1980 chunk 170 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 230 optimal weight: 0.2980 chunk 264 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 L 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.074549 restraints weight = 33273.221| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.38 r_work: 0.2779 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22641 Z= 0.103 Angle : 0.481 7.622 30602 Z= 0.258 Chirality : 0.042 0.142 3484 Planarity : 0.004 0.050 3909 Dihedral : 3.895 41.291 3105 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.71 % Allowed : 14.76 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2802 helix: 2.70 (0.16), residues: 1044 sheet: 0.92 (0.20), residues: 631 loop : -0.94 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.023 0.001 PHE L 69 TYR 0.016 0.001 TYR D 185 ARG 0.010 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1112) hydrogen bonds : angle 3.84112 ( 3195) covalent geometry : bond 0.00236 (22641) covalent geometry : angle 0.48135 (30602) ********************** 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 248 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 2.548 Fit side-chains REVERT: A 150 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8595 (t0) REVERT: B 178 ASP cc_start: 0.8157 (t70) cc_final: 0.7722 (t0) REVERT: G 145 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8053 (pm20) REVERT: I 199 ASP cc_start: 0.8314 (m-30) cc_final: 0.7907 (m-30) REVERT: I 243 ASP cc_start: 0.8250 (t70) cc_final: 0.7844 (t0) REVERT: J 131 ASP cc_start: 0.8836 (m-30) cc_final: 0.8571 (m-30) REVERT: K 31 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7494 (tptt) REVERT: L 192 LYS cc_start: 0.8387 (tttt) cc_final: 0.8069 (tptm) REVERT: M 65 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: M 98 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6988 (m-80) outliers start: 17 outliers final: 14 residues processed: 243 average time/residue: 1.6547 time to fit residues: 451.4934 Evaluate side-chains 248 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 2.531 ------------------------------------------------------------------------------- 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 G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 10 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 I 40 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 = 0.3474 r_free = 0.3474 target = 0.108830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073493 restraints weight = 33047.364| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.37 r_work: 0.2759 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22641 Z= 0.127 Angle : 0.498 7.511 30602 Z= 0.266 Chirality : 0.042 0.143 3484 Planarity : 0.005 0.054 3909 Dihedral : 3.951 39.245 3105 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.84 % Allowed : 14.68 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2802 helix: 2.66 (0.16), residues: 1044 sheet: 0.93 (0.20), residues: 623 loop : -0.97 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.025 0.001 PHE L 69 TYR 0.017 0.001 TYR K 51 ARG 0.010 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 1112) hydrogen bonds : angle 3.88255 ( 3195) covalent geometry : bond 0.00307 (22641) covalent geometry : angle 0.49822 (30602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18370.42 seconds wall clock time: 319 minutes 4.42 seconds (19144.42 seconds total)