Starting phenix.real_space_refine on Thu Apr 11 10:06:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_18758_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_18758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_18758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_18758_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qym_18758/04_2024/8qym_18758_updated.pdb" } 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 Residue "C GLU 223": "OE1" <-> "OE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22235 Number of models: 1 Model: "" Number of chains: 13 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: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1664 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 38 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: 11.64, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.80 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 83 helices and 24 sheets defined 36.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 80 through 101 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 107 through 122 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) removed outlier: 4.543A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.549A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 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 223 through 232 Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.917A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.667A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 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) removed outlier: 4.219A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'C' and resid 17 through 28 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) removed outlier: 3.516A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 77 through 97 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 104 through 119 removed outlier: 4.021A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.758A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 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 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 222 through 237 Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.873A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 103 removed outlier: 4.018A pdb=" N LYS D 86 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 103 " --> pdb=" O TRP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.678A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.557A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 removed outlier: 3.607A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 105 through 120 removed outlier: 4.195A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.678A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.840A pdb=" N VAL E 229 " --> pdb=" O ASP E 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Proline residue: E 231 - end of helix removed outlier: 3.835A pdb=" N GLU E 234 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY E 235 " --> pdb=" O PHE E 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 235' Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.708A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU F 32 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.082A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 179 removed outlier: 4.123A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 201 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 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'G' and resid 23 through 29 removed outlier: 3.509A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 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) removed outlier: 4.074A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 191 through 206 removed outlier: 3.692A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 242 Processing helix chain 'H' and resid 47 through 53 removed outlier: 4.246A pdb=" N SER H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 70 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.699A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 62 through 65 No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 77 through 86 Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 214 through 225 Processing helix chain 'I' and resid 244 through 255 removed outlier: 4.146A pdb=" N PHE I 250 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 252 - end of helix removed outlier: 4.619A pdb=" N SER I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 262 No H-bonds generated for 'chain 'I' and resid 260 through 262' Processing helix chain 'I' and resid 266 through 277 Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.125A pdb=" N VAL J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY J 28 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU J 39 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 113 Processing helix chain 'J' and resid 131 through 135 removed outlier: 3.806A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 131 through 135' Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 187 through 197 Processing helix chain 'J' and resid 214 through 228 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 19 through 32 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 113 Processing helix chain 'K' and resid 119 through 132 Processing helix chain 'K' and resid 174 through 184 Processing helix chain 'K' and resid 191 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 57 through 78 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 84 through 96 Processing helix chain 'L' and resid 143 through 153 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 160 through 172 Processing helix chain 'M' and resid 53 through 71 removed outlier: 3.835A pdb=" N ALA M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 92 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 153 through 168 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 155 through 157 removed outlier: 3.615A pdb=" N ILE A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 74 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= D, 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= E, first strand: chain 'C' and resid 158 through 161 Processing sheet with id= F, first strand: chain 'C' and resid 62 through 64 Processing sheet with id= G, first strand: chain 'D' and resid 167 through 170 Processing sheet with id= H, first strand: chain 'D' and resid 78 through 80 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= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, 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= K, first strand: chain 'F' and resid 163 through 166 Processing sheet with id= L, 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= M, 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= N, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.514A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 73 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 48 through 50 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: 6.388A pdb=" N GLN I 163 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE I 73 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR I 165 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE I 75 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU I 167 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 2 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= Q, first strand: chain 'J' and resid 17 through 20 Processing sheet with id= R, 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= S, first strand: chain 'K' and resid 162 through 164 removed outlier: 6.426A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLY K 88 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE K 77 " --> pdb=" O GLY K 88 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 136 through 140 removed outlier: 6.524A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 42 through 44 Processing sheet with id= V, first strand: chain 'M' and resid 129 through 131 Processing sheet with id= W, first strand: chain 'M' and resid 46 through 48 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) Processing sheet with id= X, 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) 969 hydrogen bonds defined for protein. 2733 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: 7.63 Time building geometry restraints manager: 9.47 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: 99.33 - 106.26: 551 106.26 - 113.20: 12268 113.20 - 120.13: 7722 120.13 - 127.07: 9863 127.07 - 134.00: 198 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: 2450 2.75 - 3.29: 19708 3.29 - 3.83: 34110 3.83 - 4.36: 40376 4.36 - 4.90: 74659 Nonbonded interactions: 171303 Sorted by model distance: nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 163 " model vdw 2.215 2.440 nonbonded pdb=" OE1 GLN C 146 " pdb=" ND2 ASN C 159 " model vdw 2.228 2.520 nonbonded pdb=" OG1 THR E 207 " pdb=" O ASP E 226 " model vdw 2.232 2.440 nonbonded pdb=" O PHE J 15 " pdb=" OG1 THR J 16 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR K 44 " pdb=" NZ LYS K 76 " model vdw 2.257 2.520 ... (remaining 171298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.040 Extract box with map and model: 7.120 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 60.340 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.550 ------------------------------------------------------------------------------- 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= 0.154 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.847 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: 1.6864 time to fit residues: 550.8668 Evaluate side-chains 240 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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: 10.0000 chunk 219 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 chunk 254 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 ASN E 90 GLN E 203 GLN F 181 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22641 Z= 0.245 Angle : 0.514 8.523 30602 Z= 0.274 Chirality : 0.043 0.152 3484 Planarity : 0.005 0.055 3909 Dihedral : 4.033 40.603 3105 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.88 % Allowed : 7.51 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.16), residues: 2802 helix: 2.40 (0.17), residues: 1021 sheet: 0.75 (0.20), residues: 615 loop : -0.92 (0.17), residues: 1166 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 0.025 0.001 PHE L 69 TYR 0.018 0.001 TYR B 136 ARG 0.008 0.000 ARG C 38 *********************** 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 266 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.806 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.8122 (t70) cc_final: 0.7880 (t0) REVERT: B 235 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7462 (tp-100) REVERT: D 168 ARG cc_start: 0.8221 (tpt-90) cc_final: 0.7902 (tpp80) REVERT: I 199 ASP cc_start: 0.8325 (m-30) cc_final: 0.8016 (m-30) REVERT: L 142 CYS cc_start: 0.8063 (m) cc_final: 0.7745 (m) REVERT: M 65 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7272 (tm-30) outliers start: 21 outliers final: 9 residues processed: 253 average time/residue: 1.7100 time to fit residues: 482.2191 Evaluate side-chains 242 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 232 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 65 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 226 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 186 HIS F 181 GLN I 40 GLN K 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1182 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= 0.306 Angle : 0.541 8.751 30602 Z= 0.288 Chirality : 0.044 0.169 3484 Planarity : 0.005 0.051 3909 Dihedral : 4.232 40.381 3105 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.34 % Allowed : 10.36 % Favored : 88.30 % 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: 0.87 (0.16), residues: 2802 helix: 2.17 (0.17), residues: 1026 sheet: 0.79 (0.20), residues: 615 loop : -1.05 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.027 0.001 PHE L 69 TYR 0.017 0.001 TYR K 51 ARG 0.005 0.000 ARG C 38 *********************** 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 fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 2.630 Fit side-chains REVERT: B 52 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 100 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: B 178 ASP cc_start: 0.8277 (t70) cc_final: 0.7987 (t0) REVERT: E 174 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7387 (tpt-90) REVERT: F 144 ASN cc_start: 0.8246 (p0) cc_final: 0.7999 (p0) REVERT: H 110 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: I 199 ASP cc_start: 0.8408 (m-30) cc_final: 0.8104 (m-30) REVERT: K 32 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7197 (mtm-85) REVERT: L 142 CYS cc_start: 0.8120 (m) cc_final: 0.7805 (m) REVERT: M 65 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7521 (tm-30) outliers start: 32 outliers final: 14 residues processed: 254 average time/residue: 1.6953 time to fit residues: 481.0735 Evaluate side-chains 243 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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 52 ILE 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 F residue 151 MET Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain L residue 168 SER 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 185 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 ASN I 40 GLN I 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22641 Z= 0.287 Angle : 0.523 8.358 30602 Z= 0.279 Chirality : 0.044 0.157 3484 Planarity : 0.005 0.050 3909 Dihedral : 4.240 41.732 3105 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.76 % Allowed : 11.32 % Favored : 86.92 % 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: 0.80 (0.16), residues: 2802 helix: 2.10 (0.17), residues: 1023 sheet: 0.74 (0.20), residues: 620 loop : -1.05 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.006 0.001 HIS I 125 PHE 0.027 0.001 PHE L 69 TYR 0.017 0.001 TYR K 51 ARG 0.009 0.000 ARG C 38 *********************** 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 272 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 2.828 Fit side-chains REVERT: B 100 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: B 178 ASP cc_start: 0.8285 (t70) cc_final: 0.7959 (t0) REVERT: B 235 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7468 (tp-100) REVERT: H 110 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: I 199 ASP cc_start: 0.8403 (m-30) cc_final: 0.8098 (m-30) REVERT: K 32 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7233 (mtm-85) REVERT: L 142 CYS cc_start: 0.8143 (m) cc_final: 0.7773 (m) REVERT: L 144 GLU cc_start: 0.8026 (pm20) cc_final: 0.7768 (pm20) REVERT: L 145 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: M 65 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7438 (tm-30) outliers start: 42 outliers final: 15 residues processed: 252 average time/residue: 1.6959 time to fit residues: 478.5061 Evaluate side-chains 242 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 100 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain E residue 56 LEU 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 H residue 110 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 145 GLN Chi-restraints excluded: chain L residue 168 SER 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 185 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 187 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN I 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22641 Z= 0.206 Angle : 0.484 7.904 30602 Z= 0.259 Chirality : 0.042 0.146 3484 Planarity : 0.005 0.049 3909 Dihedral : 4.090 39.908 3105 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.34 % Allowed : 12.70 % Favored : 85.95 % 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: 0.96 (0.16), residues: 2802 helix: 2.23 (0.17), residues: 1021 sheet: 0.81 (0.20), residues: 622 loop : -0.96 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.024 0.001 PHE L 69 TYR 0.016 0.001 TYR K 51 ARG 0.009 0.000 ARG C 38 *********************** 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 265 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 2.467 Fit side-chains REVERT: B 25 MET cc_start: 0.8579 (mtp) cc_final: 0.8275 (mtm) REVERT: B 52 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 178 ASP cc_start: 0.8195 (t70) cc_final: 0.7892 (t0) REVERT: H 110 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: I 199 ASP cc_start: 0.8379 (m-30) cc_final: 0.8070 (m-30) REVERT: L 142 CYS cc_start: 0.8149 (m) cc_final: 0.7712 (m) REVERT: L 144 GLU cc_start: 0.8040 (pm20) cc_final: 0.7778 (pm20) REVERT: L 145 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: M 65 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7438 (tm-30) outliers start: 32 outliers final: 14 residues processed: 249 average time/residue: 1.6766 time to fit residues: 467.2469 Evaluate side-chains 244 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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 52 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 55 MET 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 185 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN F 181 GLN I 40 GLN I 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22641 Z= 0.239 Angle : 0.500 8.190 30602 Z= 0.267 Chirality : 0.043 0.151 3484 Planarity : 0.005 0.048 3909 Dihedral : 4.121 40.394 3105 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.59 % Allowed : 13.50 % Favored : 84.91 % 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: 2.22 (0.17), residues: 1020 sheet: 0.81 (0.20), residues: 620 loop : -1.02 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.026 0.001 PHE L 69 TYR 0.028 0.001 TYR E 123 ARG 0.009 0.000 ARG C 38 *********************** 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 268 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 2.832 Fit side-chains REVERT: A 150 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7995 (t0) REVERT: B 25 MET cc_start: 0.8596 (mtp) cc_final: 0.8282 (mtm) REVERT: B 178 ASP cc_start: 0.8195 (t70) cc_final: 0.7887 (t0) REVERT: H 110 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: I 199 ASP cc_start: 0.8371 (m-30) cc_final: 0.8075 (m-30) REVERT: L 142 CYS cc_start: 0.8019 (m) cc_final: 0.7562 (m) REVERT: L 144 GLU cc_start: 0.8033 (pm20) cc_final: 0.7758 (pm20) REVERT: L 145 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: M 65 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7451 (tm-30) outliers start: 38 outliers final: 18 residues processed: 250 average time/residue: 1.6249 time to fit residues: 455.2351 Evaluate side-chains 251 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 E residue 207 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 144 ASP 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 159 ASN Chi-restraints excluded: chain L residue 115 LYS 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 185 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN I 40 GLN K 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22641 Z= 0.142 Angle : 0.447 6.868 30602 Z= 0.241 Chirality : 0.041 0.142 3484 Planarity : 0.004 0.049 3909 Dihedral : 3.888 37.192 3105 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.09 % Allowed : 14.09 % Favored : 84.82 % 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: 1.11 (0.16), residues: 2802 helix: 2.35 (0.17), residues: 1020 sheet: 0.85 (0.20), residues: 640 loop : -0.85 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.021 0.001 PHE L 69 TYR 0.031 0.001 TYR E 123 ARG 0.010 0.000 ARG C 38 *********************** 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 260 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.710 Fit side-chains REVERT: A 150 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7902 (t0) REVERT: B 25 MET cc_start: 0.8549 (mtp) cc_final: 0.8266 (mtm) REVERT: B 178 ASP cc_start: 0.8108 (t70) cc_final: 0.7849 (t0) REVERT: H 110 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: I 53 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8065 (mp-120) REVERT: I 199 ASP cc_start: 0.8332 (m-30) cc_final: 0.7993 (m-30) REVERT: L 142 CYS cc_start: 0.8015 (m) cc_final: 0.7751 (m) REVERT: M 65 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7225 (tm-30) outliers start: 26 outliers final: 11 residues processed: 251 average time/residue: 1.6681 time to fit residues: 467.4981 Evaluate side-chains 236 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 222 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 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 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 93 ILE Chi-restraints excluded: chain J residue 159 ASN 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 185 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 161 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN G 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22641 Z= 0.190 Angle : 0.480 9.480 30602 Z= 0.255 Chirality : 0.042 0.144 3484 Planarity : 0.004 0.048 3909 Dihedral : 3.924 38.378 3105 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.05 % Allowed : 14.34 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.17), residues: 1021 sheet: 0.87 (0.20), residues: 632 loop : -0.87 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.024 0.001 PHE L 69 TYR 0.035 0.001 TYR E 123 ARG 0.009 0.000 ARG C 38 *********************** 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 251 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.739 Fit side-chains REVERT: A 150 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7935 (t0) REVERT: B 25 MET cc_start: 0.8563 (mtp) cc_final: 0.8257 (mtm) REVERT: B 178 ASP cc_start: 0.8138 (t70) cc_final: 0.7870 (t0) REVERT: H 110 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: I 199 ASP cc_start: 0.8336 (m-30) cc_final: 0.7989 (m-30) REVERT: L 142 CYS cc_start: 0.8057 (m) cc_final: 0.7827 (m) REVERT: M 65 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7224 (tm-30) outliers start: 25 outliers final: 15 residues processed: 241 average time/residue: 1.6335 time to fit residues: 440.3667 Evaluate side-chains 242 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 207 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 159 ASN 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 185 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 10.0000 chunk 258 optimal weight: 0.0470 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN G 147 GLN I 40 GLN K 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22641 Z= 0.308 Angle : 0.540 9.045 30602 Z= 0.286 Chirality : 0.044 0.162 3484 Planarity : 0.005 0.048 3909 Dihedral : 4.198 44.003 3105 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.26 % Allowed : 14.34 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2802 helix: 2.16 (0.17), residues: 1023 sheet: 0.84 (0.20), residues: 615 loop : -1.04 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 102 HIS 0.005 0.001 HIS I 125 PHE 0.025 0.001 PHE L 69 TYR 0.033 0.002 TYR E 123 ARG 0.010 0.000 ARG C 38 *********************** 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 255 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 2.940 Fit side-chains REVERT: A 150 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (t0) REVERT: B 178 ASP cc_start: 0.8208 (t70) cc_final: 0.7919 (t0) REVERT: H 110 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: I 53 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8025 (mp-120) REVERT: I 199 ASP cc_start: 0.8368 (m-30) cc_final: 0.8031 (m-30) REVERT: L 142 CYS cc_start: 0.8102 (m) cc_final: 0.7843 (m) REVERT: M 65 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7533 (tm-30) outliers start: 30 outliers final: 17 residues processed: 244 average time/residue: 1.6182 time to fit residues: 442.2967 Evaluate side-chains 241 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 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 E residue 207 THR 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 49 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 168 SER 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 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 222 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN G 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1390 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= 0.174 Angle : 0.478 9.296 30602 Z= 0.255 Chirality : 0.042 0.143 3484 Planarity : 0.004 0.048 3909 Dihedral : 4.008 44.813 3105 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.96 % Allowed : 14.76 % Favored : 84.28 % 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: 1.02 (0.16), residues: 2802 helix: 2.29 (0.17), residues: 1020 sheet: 0.87 (0.20), residues: 624 loop : -0.94 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.023 0.001 PHE L 69 TYR 0.033 0.001 TYR E 123 ARG 0.009 0.000 ARG C 38 ********************** 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 247 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 224 time to evaluate : 2.890 Fit side-chains REVERT: A 150 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7939 (t0) REVERT: B 25 MET cc_start: 0.8561 (mtp) cc_final: 0.8277 (mtm) REVERT: B 178 ASP cc_start: 0.8156 (t70) cc_final: 0.7861 (t0) REVERT: H 110 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: I 53 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8010 (mp-120) REVERT: I 199 ASP cc_start: 0.8363 (m-30) cc_final: 0.8022 (m-30) REVERT: L 142 CYS cc_start: 0.8076 (m) cc_final: 0.7848 (m) REVERT: M 65 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7299 (tm-30) outliers start: 23 outliers final: 16 residues processed: 239 average time/residue: 1.6409 time to fit residues: 439.0810 Evaluate side-chains 241 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 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 E residue 207 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 168 SER 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 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN D 214 ASN F 144 ASN G 147 GLN K 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079437 restraints weight = 35923.923| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.34 r_work: 0.2893 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22641 Z= 0.270 Angle : 0.523 9.066 30602 Z= 0.278 Chirality : 0.043 0.155 3484 Planarity : 0.005 0.047 3909 Dihedral : 4.152 45.749 3105 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.17 % Allowed : 14.55 % Favored : 84.28 % 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: 0.92 (0.16), residues: 2802 helix: 2.20 (0.17), residues: 1022 sheet: 0.84 (0.20), residues: 620 loop : -1.01 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.005 0.001 HIS I 125 PHE 0.027 0.001 PHE L 69 TYR 0.028 0.001 TYR E 123 ARG 0.010 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8386.73 seconds wall clock time: 150 minutes 50.50 seconds (9050.50 seconds total)