Starting phenix.real_space_refine on Fri Mar 15 10:10:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e26_30952/03_2024/7e26_30952.pdb" } resolution = 2.29 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= 0.006 sd= 0.066 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 70 5.16 5 C 7515 2.51 5 N 1765 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 6.35, per 1000 atoms: 0.56 Number of scatterers: 11360 At special positions: 0 Unit cell: (96.4678, 96.4678, 82.9758, 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 70 16.00 O 2010 8.00 N 1765 7.00 C 7515 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: 4.30 Conformation dependent library (CDL) restraints added in 2.0 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 81.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE D 169 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.976A pdb=" N SER D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 291 removed outlier: 3.515A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.864A pdb=" N PHE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.976A pdb=" N SER A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.515A pdb=" N GLY A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 removed outlier: 3.866A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.520A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.976A pdb=" N SER B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.574A pdb=" N ASN B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.510A pdb=" N LYS C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.443A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.763A pdb=" N PHE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 227 removed outlier: 3.977A pdb=" N SER C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 91 through 101 removed outlier: 4.070A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 removed outlier: 3.977A pdb=" N SER E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 7.314A pdb=" N SER B 14 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE C 15 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 16 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER A 14 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE B 15 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS A 16 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL A 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER D 14 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E 15 " --> pdb=" O SER D 14 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS D 16 " --> pdb=" O ILE E 15 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.25: 1675 1.25 - 1.39: 3321 1.39 - 1.53: 5983 1.53 - 1.67: 496 1.67 - 1.81: 100 Bond restraints: 11575 Sorted by residual: bond pdb=" C HIS A 230 " pdb=" O HIS A 230 " ideal model delta sigma weight residual 1.235 1.116 0.118 1.18e-02 7.18e+03 1.01e+02 bond pdb=" C HIS B 284 " pdb=" O HIS B 284 " ideal model delta sigma weight residual 1.237 1.126 0.110 1.19e-02 7.06e+03 8.57e+01 bond pdb=" C LEU A 259 " pdb=" O LEU A 259 " ideal model delta sigma weight residual 1.244 1.159 0.084 9.40e-03 1.13e+04 8.02e+01 bond pdb=" C ASN B 287 " pdb=" O ASN B 287 " ideal model delta sigma weight residual 1.237 1.150 0.086 1.16e-02 7.43e+03 5.55e+01 bond pdb=" CA HIS B 284 " pdb=" C HIS B 284 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.29e-02 6.01e+03 5.47e+01 ... (remaining 11570 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.14: 136 106.14 - 112.71: 5704 112.71 - 119.29: 3496 119.29 - 125.87: 6284 125.87 - 132.45: 70 Bond angle restraints: 15690 Sorted by residual: angle pdb=" N ARG D 290 " pdb=" CA ARG D 290 " pdb=" C ARG D 290 " ideal model delta sigma weight residual 112.23 103.87 8.36 1.26e+00 6.30e-01 4.40e+01 angle pdb=" N THR B 181 " pdb=" CA THR B 181 " pdb=" C THR B 181 " ideal model delta sigma weight residual 110.36 102.22 8.14 1.55e+00 4.16e-01 2.76e+01 angle pdb=" N HIS A 179 " pdb=" CA HIS A 179 " pdb=" C HIS A 179 " ideal model delta sigma weight residual 112.92 119.19 -6.27 1.23e+00 6.61e-01 2.60e+01 angle pdb=" N THR A 181 " pdb=" CA THR A 181 " pdb=" C THR A 181 " ideal model delta sigma weight residual 110.59 103.55 7.04 1.45e+00 4.76e-01 2.36e+01 angle pdb=" CA HIS A 230 " pdb=" C HIS A 230 " pdb=" N ILE A 231 " ideal model delta sigma weight residual 115.96 122.22 -6.26 1.29e+00 6.01e-01 2.35e+01 ... (remaining 15685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 5840 15.85 - 31.70: 600 31.70 - 47.55: 92 47.55 - 63.40: 48 63.40 - 79.25: 10 Dihedral angle restraints: 6590 sinusoidal: 2395 harmonic: 4195 Sorted by residual: dihedral pdb=" C HIS A 179 " pdb=" N HIS A 179 " pdb=" CA HIS A 179 " pdb=" CB HIS A 179 " ideal model delta harmonic sigma weight residual -122.60 -132.17 9.57 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C HIS C 179 " pdb=" N HIS C 179 " pdb=" CA HIS C 179 " pdb=" CB HIS C 179 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N HIS A 179 " pdb=" C HIS A 179 " pdb=" CA HIS A 179 " pdb=" CB HIS A 179 " ideal model delta harmonic sigma weight residual 122.80 131.74 -8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 6587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1619 0.093 - 0.187: 140 0.187 - 0.280: 20 0.280 - 0.373: 2 0.373 - 0.466: 9 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA HIS A 179 " pdb=" N HIS A 179 " pdb=" C HIS A 179 " pdb=" CB HIS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA PHE C 94 " pdb=" N PHE C 94 " pdb=" C PHE C 94 " pdb=" CB PHE C 94 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA PHE E 94 " pdb=" N PHE E 94 " pdb=" C PHE E 94 " pdb=" CB PHE E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1787 not shown) Planarity restraints: 1915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.032 2.00e-02 2.50e+03 2.20e-02 8.45e+00 pdb=" CG PHE D 94 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 284 " -0.027 2.00e-02 2.50e+03 2.35e-02 8.31e+00 pdb=" CG HIS B 284 " 0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS B 284 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 284 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 284 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 284 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " -0.030 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE E 94 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 1912 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3636 2.83 - 3.35: 10417 3.35 - 3.86: 20716 3.86 - 4.38: 25001 4.38 - 4.90: 42248 Nonbonded interactions: 102018 Sorted by model distance: nonbonded pdb=" OH TYR A 25 " pdb=" OE2 GLU A 118 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR D 25 " pdb=" OE2 GLU D 118 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR B 25 " pdb=" OE2 GLU B 118 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR E 25 " pdb=" OE2 GLU E 118 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR C 25 " pdb=" OE2 GLU C 118 " model vdw 2.314 2.440 ... (remaining 102013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.780 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 31.310 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.009 0.118 11575 Z= 0.561 Angle : 0.931 9.042 15690 Z= 0.565 Chirality : 0.064 0.466 1790 Planarity : 0.006 0.033 1915 Dihedral : 14.053 79.249 3940 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.19 % Allowed : 2.37 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.93 (0.17), residues: 1425 helix: -1.59 (0.12), residues: 1140 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS B 284 PHE 0.047 0.004 PHE E 94 TYR 0.044 0.003 TYR C 212 ARG 0.006 0.001 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.220 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 1.2995 time to fit residues: 196.1794 Evaluate side-chains 101 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11575 Z= 0.138 Angle : 0.464 7.561 15690 Z= 0.255 Chirality : 0.036 0.142 1790 Planarity : 0.003 0.022 1915 Dihedral : 5.495 49.655 1587 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.88 % Allowed : 6.02 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.21), residues: 1425 helix: 0.43 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.06 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 59 PHE 0.019 0.001 PHE E 223 TYR 0.012 0.001 TYR E 236 ARG 0.001 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 1.304 Fit side-chains REVERT: B 124 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8053 (mp) REVERT: B 243 MET cc_start: 0.8745 (mtt) cc_final: 0.8534 (mtt) outliers start: 34 outliers final: 7 residues processed: 127 average time/residue: 1.1696 time to fit residues: 161.8361 Evaluate side-chains 97 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.0570 chunk 137 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11575 Z= 0.234 Angle : 0.523 7.564 15690 Z= 0.286 Chirality : 0.040 0.152 1790 Planarity : 0.003 0.021 1915 Dihedral : 4.621 43.426 1572 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.71 % Allowed : 8.73 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.22), residues: 1425 helix: 1.00 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 59 PHE 0.017 0.002 PHE D 223 TYR 0.015 0.002 TYR A 212 ARG 0.001 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.348 Fit side-chains REVERT: C 119 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7877 (mttp) REVERT: E 42 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7689 (t0) outliers start: 32 outliers final: 16 residues processed: 117 average time/residue: 1.2337 time to fit residues: 157.3043 Evaluate side-chains 108 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11575 Z= 0.395 Angle : 0.606 7.830 15690 Z= 0.332 Chirality : 0.045 0.165 1790 Planarity : 0.003 0.023 1915 Dihedral : 4.728 17.877 1570 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.39 % Allowed : 10.34 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1425 helix: 0.94 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 59 PHE 0.021 0.003 PHE D 223 TYR 0.015 0.002 TYR A 69 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 1.531 Fit side-chains REVERT: A 42 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7967 (t0) REVERT: B 42 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7867 (t0) REVERT: B 124 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 42 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.8011 (t0) REVERT: C 119 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7822 (mttp) REVERT: E 42 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7804 (t0) outliers start: 40 outliers final: 22 residues processed: 125 average time/residue: 1.2307 time to fit residues: 167.5992 Evaluate side-chains 120 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11575 Z= 0.189 Angle : 0.495 7.512 15690 Z= 0.272 Chirality : 0.038 0.145 1790 Planarity : 0.003 0.022 1915 Dihedral : 4.394 18.539 1570 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.88 % Allowed : 11.44 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1425 helix: 1.33 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 180 PHE 0.015 0.002 PHE D 223 TYR 0.011 0.001 TYR C 236 ARG 0.001 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 1.174 Fit side-chains REVERT: A 42 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 42 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7629 (t0) REVERT: B 124 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 201 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 243 MET cc_start: 0.8776 (mtt) cc_final: 0.8377 (mtt) REVERT: C 42 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7732 (t0) REVERT: E 42 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7596 (t0) outliers start: 34 outliers final: 18 residues processed: 121 average time/residue: 1.1475 time to fit residues: 151.6455 Evaluate side-chains 118 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11575 Z= 0.155 Angle : 0.469 7.518 15690 Z= 0.257 Chirality : 0.037 0.138 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.209 18.918 1570 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.05 % Allowed : 11.78 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.22), residues: 1425 helix: 1.59 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.88 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 180 PHE 0.014 0.001 PHE D 223 TYR 0.011 0.001 TYR C 251 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.229 Fit side-chains REVERT: D 119 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7990 (mttt) REVERT: A 42 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7612 (t0) REVERT: B 124 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 201 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8212 (t80) REVERT: B 243 MET cc_start: 0.8794 (mtt) cc_final: 0.8404 (mtt) REVERT: C 42 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7572 (t0) REVERT: C 119 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: E 42 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7585 (t0) outliers start: 36 outliers final: 14 residues processed: 127 average time/residue: 1.0989 time to fit residues: 152.3921 Evaluate side-chains 119 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 0.0000 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11575 Z= 0.193 Angle : 0.494 7.871 15690 Z= 0.269 Chirality : 0.038 0.144 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.285 18.584 1570 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.80 % Allowed : 11.95 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1425 helix: 1.54 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 180 PHE 0.015 0.002 PHE D 223 TYR 0.011 0.001 TYR B 31 ARG 0.001 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.232 Fit side-chains REVERT: D 119 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8001 (mttt) REVERT: A 42 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7719 (t0) REVERT: B 42 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (t0) REVERT: B 124 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 201 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (t80) REVERT: B 243 MET cc_start: 0.8787 (mtt) cc_final: 0.8431 (mtt) REVERT: C 42 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7753 (t0) REVERT: C 119 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7835 (mttt) REVERT: E 42 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7574 (t0) outliers start: 33 outliers final: 19 residues processed: 125 average time/residue: 1.1168 time to fit residues: 152.7872 Evaluate side-chains 125 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11575 Z= 0.238 Angle : 0.523 8.421 15690 Z= 0.285 Chirality : 0.040 0.149 1790 Planarity : 0.003 0.021 1915 Dihedral : 4.385 18.193 1570 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.31 % Allowed : 11.36 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.22), residues: 1425 helix: 1.45 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 180 PHE 0.016 0.002 PHE D 223 TYR 0.011 0.002 TYR B 31 ARG 0.001 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.308 Fit side-chains REVERT: D 119 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7972 (mttp) REVERT: A 42 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7786 (t0) REVERT: B 124 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 243 MET cc_start: 0.8792 (mtt) cc_final: 0.8389 (mtt) REVERT: C 42 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (t0) REVERT: C 119 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7841 (mttt) REVERT: E 42 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7664 (t0) outliers start: 39 outliers final: 20 residues processed: 130 average time/residue: 1.1493 time to fit residues: 163.1074 Evaluate side-chains 125 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11575 Z= 0.149 Angle : 0.471 8.592 15690 Z= 0.256 Chirality : 0.037 0.138 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.144 18.728 1570 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.54 % Allowed : 12.12 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.22), residues: 1425 helix: 1.67 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 59 PHE 0.013 0.001 PHE D 223 TYR 0.012 0.001 TYR C 251 ARG 0.001 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.275 Fit side-chains REVERT: D 119 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7957 (mttt) REVERT: A 42 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7606 (t0) REVERT: B 124 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 243 MET cc_start: 0.8799 (mtt) cc_final: 0.8422 (mtt) REVERT: C 42 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7564 (t0) REVERT: C 119 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7822 (mttt) REVERT: E 42 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7577 (t0) outliers start: 30 outliers final: 15 residues processed: 124 average time/residue: 1.2155 time to fit residues: 164.0854 Evaluate side-chains 120 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11575 Z= 0.148 Angle : 0.469 8.819 15690 Z= 0.253 Chirality : 0.037 0.137 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.094 18.640 1570 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.95 % Allowed : 12.88 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.22), residues: 1425 helix: 1.74 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 59 PHE 0.013 0.001 PHE A 223 TYR 0.012 0.001 TYR C 251 ARG 0.001 0.000 ARG E 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.075 Fit side-chains REVERT: D 119 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7948 (mttt) REVERT: A 42 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 124 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 243 MET cc_start: 0.8804 (mtt) cc_final: 0.8431 (mtt) REVERT: C 119 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7811 (mttt) REVERT: E 42 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 23 outliers final: 16 residues processed: 121 average time/residue: 1.2498 time to fit residues: 163.9764 Evaluate side-chains 120 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 291 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.083777 restraints weight = 13947.650| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.72 r_work: 0.2877 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11575 Z= 0.189 Angle : 0.497 9.754 15690 Z= 0.268 Chirality : 0.038 0.143 1790 Planarity : 0.002 0.021 1915 Dihedral : 4.220 18.440 1570 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.12 % Allowed : 12.80 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.22), residues: 1425 helix: 1.65 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 180 PHE 0.014 0.002 PHE D 223 TYR 0.011 0.001 TYR B 31 ARG 0.000 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3533.04 seconds wall clock time: 63 minutes 59.68 seconds (3839.68 seconds total)