Starting phenix.real_space_refine on Mon Mar 11 08:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/03_2024/7p3r_13185.pdb" } resolution = 3.65 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= 0.000 sd= 0.004 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 8 5.16 5 C 4702 2.51 5 N 1454 2.21 5 O 1574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7738 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1902 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 6, 'TRANS': 321} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 722 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 273 Chain: "B" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1967 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 6, 'TRANS': 334} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 289 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1902 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 6, 'TRANS': 321} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 722 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 273 Chain: "D" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1967 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 6, 'TRANS': 334} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 289 Time building chain proxies: 4.88, per 1000 atoms: 0.63 Number of scatterers: 7738 At special positions: 0 Unit cell: (157.342, 128.166, 110.452, 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 8 16.00 O 1574 8.00 N 1454 7.00 C 4702 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: 3.33 Conformation dependent library (CDL) restraints added in 2.0 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.964A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.185A pdb=" N LYS A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.532A pdb=" N ILE A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 removed outlier: 3.675A pdb=" N ALA A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 158 removed outlier: 4.124A pdb=" N ILE A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 217 removed outlier: 3.904A pdb=" N TYR A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 315 removed outlier: 3.863A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 4.382A pdb=" N ILE A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.694A pdb=" N THR B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.663A pdb=" N ALA B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.656A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 removed outlier: 4.025A pdb=" N VAL B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 157 removed outlier: 3.514A pdb=" N GLN B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 217 removed outlier: 4.073A pdb=" N TYR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 319 removed outlier: 3.560A pdb=" N ALA B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 328 removed outlier: 3.631A pdb=" N ILE B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 349 removed outlier: 4.193A pdb=" N LYS B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 Processing helix chain 'C' and resid 46 through 67 Processing helix chain 'C' and resid 67 through 85 removed outlier: 3.965A pdb=" N ILE C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Proline residue: C 77 - end of helix removed outlier: 3.812A pdb=" N ASN C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 101 removed outlier: 3.577A pdb=" N TYR C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 126 removed outlier: 3.784A pdb=" N SER C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 216 removed outlier: 3.981A pdb=" N ASN C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 316 removed outlier: 4.102A pdb=" N ILE C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 272 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 345 removed outlier: 6.171A pdb=" N LYS C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 343 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 35 removed outlier: 3.580A pdb=" N VAL D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 67 removed outlier: 4.152A pdb=" N LYS D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.890A pdb=" N SER D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.584A pdb=" N ALA D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 156 removed outlier: 3.992A pdb=" N ASP D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 218 removed outlier: 3.910A pdb=" N PHE D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 319 removed outlier: 3.629A pdb=" N ALA D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.936A pdb=" N ILE D 326 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 349 removed outlier: 4.015A pdb=" N VAL D 343 " --> pdb=" O TRP D 339 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2811 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: 2.39 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2589 1.34 - 1.45: 578 1.45 - 1.57: 4571 1.57 - 1.68: 0 1.68 - 1.80: 16 Bond restraints: 7754 Sorted by residual: bond pdb=" C ILE C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.25e-02 6.40e+03 1.60e+01 bond pdb=" CB THR C 242 " pdb=" CG2 THR C 242 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.69e+00 bond pdb=" CB ILE A 237 " pdb=" CG2 ILE A 237 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.30e+00 bond pdb=" CB ILE A 236 " pdb=" CG2 ILE A 236 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB VAL D 208 " pdb=" CG1 VAL D 208 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.19: 41 106.19 - 113.11: 4416 113.11 - 120.03: 2785 120.03 - 126.96: 3435 126.96 - 133.88: 13 Bond angle restraints: 10690 Sorted by residual: angle pdb=" C PHE B 37 " pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 120.69 130.62 -9.93 2.95e+00 1.15e-01 1.13e+01 angle pdb=" N ILE A 76 " pdb=" CA ILE A 76 " pdb=" C ILE A 76 " ideal model delta sigma weight residual 108.88 115.88 -7.00 2.16e+00 2.14e-01 1.05e+01 angle pdb=" C ASP A 252 " pdb=" N ASP A 253 " pdb=" CA ASP A 253 " ideal model delta sigma weight residual 122.06 116.16 5.90 1.86e+00 2.89e-01 1.01e+01 angle pdb=" N ILE C 76 " pdb=" CA ILE C 76 " pdb=" C ILE C 76 " ideal model delta sigma weight residual 108.88 115.72 -6.84 2.16e+00 2.14e-01 1.00e+01 angle pdb=" N VAL D 155 " pdb=" CA VAL D 155 " pdb=" CB VAL D 155 " ideal model delta sigma weight residual 111.75 103.19 8.56 2.73e+00 1.34e-01 9.84e+00 ... (remaining 10685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4337 17.38 - 34.76: 214 34.76 - 52.14: 44 52.14 - 69.52: 8 69.52 - 86.90: 11 Dihedral angle restraints: 4614 sinusoidal: 748 harmonic: 3866 Sorted by residual: dihedral pdb=" CA ASP D 84 " pdb=" C ASP D 84 " pdb=" N ALA D 85 " pdb=" CA ALA D 85 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LEU D 50 " pdb=" C LEU D 50 " pdb=" N SER D 51 " pdb=" CA SER D 51 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASP D 67 " pdb=" C ASP D 67 " pdb=" N LEU D 68 " pdb=" CA LEU D 68 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1124 0.056 - 0.112: 247 0.112 - 0.168: 38 0.168 - 0.224: 7 0.224 - 0.280: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB ILE A 236 " pdb=" CA ILE A 236 " pdb=" CG1 ILE A 236 " pdb=" CG2 ILE A 236 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL D 208 " pdb=" CA VAL D 208 " pdb=" CG1 VAL D 208 " pdb=" CG2 VAL D 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE C 236 " pdb=" CA ILE C 236 " pdb=" CG1 ILE C 236 " pdb=" CG2 ILE C 236 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1415 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 237 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C ILE A 237 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 237 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 238 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 62 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C LYS B 62 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS B 62 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN B 63 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 208 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C VAL D 208 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL D 208 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 209 " -0.013 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2591 2.83 - 3.34: 7795 3.34 - 3.86: 12977 3.86 - 4.38: 13335 4.38 - 4.90: 22463 Nonbonded interactions: 59161 Sorted by model distance: nonbonded pdb=" O ALA D 221 " pdb=" OG SER D 225 " model vdw 2.306 2.440 nonbonded pdb=" O ALA B 238 " pdb=" OG1 THR B 242 " model vdw 2.312 2.440 nonbonded pdb=" O GLY A 210 " pdb=" OG1 THR A 214 " model vdw 2.322 2.440 nonbonded pdb=" OG1 THR B 214 " pdb=" OG SER B 225 " model vdw 2.348 2.440 nonbonded pdb=" O TRP A 64 " pdb=" N GLY A 69 " model vdw 2.351 2.520 ... (remaining 59156 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' and resid 19 through 346) selection = chain 'C' selection = (chain 'D' and resid 19 through 346) } 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 group one per residue 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: 5.790 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: 20.440 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.430 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 7754 Z= 0.393 Angle : 0.806 9.928 10690 Z= 0.508 Chirality : 0.049 0.280 1418 Planarity : 0.006 0.023 1486 Dihedral : 13.657 86.902 2090 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.28 % Allowed : 9.55 % Favored : 90.17 % Cbeta Deviations : 0.08 % 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: -3.67 (0.17), residues: 1330 helix: -2.13 (0.11), residues: 1151 sheet: None (None), residues: 0 loop : -2.75 (0.38), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 243 PHE 0.007 0.001 PHE A 205 TYR 0.010 0.002 TYR C 254 ARG 0.003 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.878 Fit side-chains REVERT: A 163 LYS cc_start: 0.8008 (mttt) cc_final: 0.7742 (mtpt) REVERT: A 187 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 248 ASN cc_start: 0.8239 (t0) cc_final: 0.7511 (m-40) REVERT: B 171 ASP cc_start: 0.8350 (t70) cc_final: 0.8032 (t70) REVERT: B 173 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 272 ILE cc_start: 0.8700 (pt) cc_final: 0.8498 (mm) REVERT: C 160 ASN cc_start: 0.7470 (m-40) cc_final: 0.7260 (m-40) REVERT: C 191 LYS cc_start: 0.8923 (tptt) cc_final: 0.8628 (tppt) REVERT: D 251 ASP cc_start: 0.7231 (m-30) cc_final: 0.6820 (m-30) REVERT: D 275 GLN cc_start: 0.6986 (tp40) cc_final: 0.6608 (mm110) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1718 time to fit residues: 27.9549 Evaluate side-chains 95 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 50.0000 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 62 optimal weight: 50.0000 chunk 77 optimal weight: 40.0000 chunk 119 optimal weight: 1.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 263 GLN C 177 ASN C 248 ASN C 249 GLN C 270 GLN D 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7754 Z= 0.314 Angle : 0.506 5.588 10690 Z= 0.306 Chirality : 0.038 0.152 1418 Planarity : 0.003 0.016 1486 Dihedral : 4.884 23.353 1346 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.09 % Allowed : 19.66 % Favored : 77.25 % 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: -0.53 (0.21), residues: 1330 helix: 0.05 (0.14), residues: 1148 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 243 PHE 0.011 0.001 PHE A 205 TYR 0.010 0.001 TYR B 254 ARG 0.001 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7485 (tp30) REVERT: A 237 ILE cc_start: 0.8411 (tp) cc_final: 0.8145 (mt) REVERT: A 248 ASN cc_start: 0.8254 (t0) cc_final: 0.7547 (m-40) REVERT: B 173 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7448 (tm-30) REVERT: C 188 LYS cc_start: 0.8104 (tttt) cc_final: 0.7848 (ttmm) REVERT: C 191 LYS cc_start: 0.8863 (tptt) cc_final: 0.8633 (tppt) REVERT: C 213 LEU cc_start: 0.9050 (tp) cc_final: 0.8837 (tp) REVERT: D 175 MET cc_start: 0.7026 (mmt) cc_final: 0.6823 (mmt) REVERT: D 191 LYS cc_start: 0.8444 (mptt) cc_final: 0.8090 (mppt) REVERT: D 251 ASP cc_start: 0.7155 (m-30) cc_final: 0.6794 (m-30) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.1770 time to fit residues: 28.6775 Evaluate side-chains 105 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7754 Z= 0.346 Angle : 0.514 7.046 10690 Z= 0.306 Chirality : 0.041 0.212 1418 Planarity : 0.003 0.016 1486 Dihedral : 4.695 23.655 1346 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 7.87 % Allowed : 19.94 % Favored : 72.19 % 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: 0.87 (0.22), residues: 1330 helix: 0.98 (0.14), residues: 1153 sheet: None (None), residues: 0 loop : -1.66 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 243 PHE 0.011 0.001 PHE A 205 TYR 0.010 0.002 TYR D 254 ARG 0.003 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.847 Fit side-chains REVERT: A 166 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 187 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7463 (tp30) REVERT: A 237 ILE cc_start: 0.8320 (tp) cc_final: 0.8066 (mt) REVERT: B 173 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 204 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8860 (tp) REVERT: C 188 LYS cc_start: 0.8109 (tttt) cc_final: 0.7845 (ttmm) REVERT: C 191 LYS cc_start: 0.8773 (tptt) cc_final: 0.8545 (tppt) REVERT: D 191 LYS cc_start: 0.8454 (mptt) cc_final: 0.8077 (mppt) REVERT: D 253 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7770 (t0) outliers start: 28 outliers final: 14 residues processed: 113 average time/residue: 0.1631 time to fit residues: 26.2378 Evaluate side-chains 107 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 253 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 13 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7754 Z= 0.195 Angle : 0.410 5.241 10690 Z= 0.246 Chirality : 0.036 0.177 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.194 19.787 1346 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.78 % Allowed : 25.28 % Favored : 69.94 % 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: 2.08 (0.22), residues: 1330 helix: 1.79 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.51 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 PHE 0.008 0.001 PHE A 205 TYR 0.010 0.001 TYR D 254 ARG 0.002 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.757 Fit side-chains REVERT: A 187 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7488 (tp30) REVERT: A 248 ASN cc_start: 0.8237 (t0) cc_final: 0.7518 (m-40) REVERT: B 171 ASP cc_start: 0.8383 (t70) cc_final: 0.8101 (t70) REVERT: B 173 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7355 (tm-30) REVERT: C 188 LYS cc_start: 0.8096 (tttt) cc_final: 0.7815 (ttmm) REVERT: C 191 LYS cc_start: 0.8752 (tptt) cc_final: 0.8523 (tppt) REVERT: D 191 LYS cc_start: 0.8378 (mptt) cc_final: 0.7955 (mppt) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.1610 time to fit residues: 25.4524 Evaluate side-chains 109 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 50.0000 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 50.0000 chunk 42 optimal weight: 50.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7754 Z= 0.222 Angle : 0.429 6.002 10690 Z= 0.254 Chirality : 0.037 0.163 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.091 22.081 1346 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.74 % Allowed : 25.84 % Favored : 67.42 % 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: 2.61 (0.22), residues: 1330 helix: 2.16 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.49 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 243 PHE 0.009 0.001 PHE B 205 TYR 0.011 0.001 TYR A 195 ARG 0.002 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.844 Fit side-chains REVERT: A 166 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 187 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7515 (tp30) REVERT: A 237 ILE cc_start: 0.8459 (tp) cc_final: 0.8256 (mt) REVERT: B 171 ASP cc_start: 0.8361 (t70) cc_final: 0.8138 (t70) REVERT: B 263 GLN cc_start: 0.7559 (tp40) cc_final: 0.7281 (tt0) REVERT: C 188 LYS cc_start: 0.8104 (tttt) cc_final: 0.7821 (ttmm) REVERT: C 191 LYS cc_start: 0.8741 (tptt) cc_final: 0.8506 (tppt) REVERT: D 191 LYS cc_start: 0.8389 (mptt) cc_final: 0.7953 (mppt) outliers start: 24 outliers final: 16 residues processed: 114 average time/residue: 0.1665 time to fit residues: 27.0095 Evaluate side-chains 115 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 270 GLN C 259 GLN D 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7754 Z= 0.360 Angle : 0.513 8.933 10690 Z= 0.302 Chirality : 0.040 0.178 1418 Planarity : 0.002 0.016 1486 Dihedral : 4.487 23.766 1346 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.30 % Allowed : 25.56 % Favored : 67.13 % 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: 2.14 (0.22), residues: 1330 helix: 1.84 (0.14), residues: 1161 sheet: None (None), residues: 0 loop : -1.50 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 243 PHE 0.012 0.001 PHE A 205 TYR 0.009 0.002 TYR D 254 ARG 0.002 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.871 Fit side-chains REVERT: A 187 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 237 ILE cc_start: 0.8557 (tp) cc_final: 0.8335 (mt) REVERT: A 259 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 171 ASP cc_start: 0.8399 (t70) cc_final: 0.8114 (t70) REVERT: C 188 LYS cc_start: 0.8138 (tttt) cc_final: 0.7899 (ttmm) REVERT: C 191 LYS cc_start: 0.8738 (tptt) cc_final: 0.8512 (tppt) REVERT: D 191 LYS cc_start: 0.8467 (mptt) cc_final: 0.8059 (mppt) REVERT: D 251 ASP cc_start: 0.7120 (m-30) cc_final: 0.6783 (m-30) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 0.1646 time to fit residues: 27.6977 Evaluate side-chains 114 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 256 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 71 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7754 Z= 0.258 Angle : 0.451 6.282 10690 Z= 0.266 Chirality : 0.038 0.177 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.176 22.114 1346 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 7.58 % Allowed : 25.28 % Favored : 67.13 % 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: 2.72 (0.23), residues: 1330 helix: 2.21 (0.15), residues: 1161 sheet: None (None), residues: 0 loop : -1.22 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 243 PHE 0.008 0.001 PHE A 205 TYR 0.009 0.001 TYR D 254 ARG 0.002 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.877 Fit side-chains REVERT: A 166 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 237 ILE cc_start: 0.8502 (tp) cc_final: 0.8275 (mt) REVERT: B 171 ASP cc_start: 0.8400 (t70) cc_final: 0.8107 (t70) REVERT: B 191 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8310 (mmtp) REVERT: C 188 LYS cc_start: 0.8133 (tttt) cc_final: 0.7830 (ttmm) REVERT: C 191 LYS cc_start: 0.8724 (tptt) cc_final: 0.8502 (tppt) REVERT: D 191 LYS cc_start: 0.8398 (mptt) cc_final: 0.7979 (mppt) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.1665 time to fit residues: 28.1709 Evaluate side-chains 120 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 50.0000 chunk 38 optimal weight: 0.0040 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7754 Z= 0.223 Angle : 0.435 5.962 10690 Z= 0.257 Chirality : 0.037 0.172 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.024 20.699 1346 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.46 % Allowed : 27.25 % Favored : 66.29 % 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: 3.11 (0.23), residues: 1330 helix: 2.48 (0.14), residues: 1163 sheet: None (None), residues: 0 loop : -1.17 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 243 PHE 0.008 0.001 PHE A 205 TYR 0.009 0.001 TYR D 254 ARG 0.001 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.761 Fit side-chains REVERT: A 166 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 237 ILE cc_start: 0.8476 (tp) cc_final: 0.8269 (mt) REVERT: A 259 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 171 ASP cc_start: 0.8382 (t70) cc_final: 0.8091 (t70) REVERT: B 191 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8299 (mmtp) REVERT: C 188 LYS cc_start: 0.8099 (tttt) cc_final: 0.7817 (ttmm) REVERT: C 191 LYS cc_start: 0.8721 (tptt) cc_final: 0.8496 (tppt) REVERT: D 191 LYS cc_start: 0.8376 (mptt) cc_final: 0.7953 (mppt) outliers start: 23 outliers final: 20 residues processed: 117 average time/residue: 0.1604 time to fit residues: 26.9491 Evaluate side-chains 121 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 107 optimal weight: 0.0170 chunk 112 optimal weight: 50.0000 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7754 Z= 0.197 Angle : 0.421 5.215 10690 Z= 0.248 Chirality : 0.036 0.175 1418 Planarity : 0.002 0.015 1486 Dihedral : 3.859 20.560 1346 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 6.46 % Allowed : 27.25 % Favored : 66.29 % 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: 3.46 (0.23), residues: 1330 helix: 2.72 (0.14), residues: 1163 sheet: None (None), residues: 0 loop : -1.08 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 243 PHE 0.008 0.001 PHE A 205 TYR 0.009 0.001 TYR D 254 ARG 0.002 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.847 Fit side-chains REVERT: A 166 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 187 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 237 ILE cc_start: 0.8591 (tp) cc_final: 0.8384 (mt) REVERT: A 248 ASN cc_start: 0.8248 (t0) cc_final: 0.7547 (m-40) REVERT: B 171 ASP cc_start: 0.8300 (t70) cc_final: 0.8028 (t70) REVERT: B 191 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8217 (mmtp) REVERT: C 188 LYS cc_start: 0.8108 (tttt) cc_final: 0.7832 (ttmm) REVERT: C 191 LYS cc_start: 0.8740 (tptt) cc_final: 0.8510 (tppt) REVERT: D 176 ASN cc_start: 0.7550 (t0) cc_final: 0.7314 (t0) REVERT: D 191 LYS cc_start: 0.8345 (mptt) cc_final: 0.7920 (mppt) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.1619 time to fit residues: 28.9123 Evaluate side-chains 123 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 256 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 80.0000 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 50.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7754 Z= 0.168 Angle : 0.408 5.255 10690 Z= 0.240 Chirality : 0.036 0.176 1418 Planarity : 0.002 0.014 1486 Dihedral : 3.723 18.875 1346 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.06 % Allowed : 28.93 % Favored : 66.01 % 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: 3.80 (0.23), residues: 1330 helix: 2.95 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 243 PHE 0.007 0.001 PHE A 205 TYR 0.009 0.001 TYR D 254 ARG 0.001 0.000 ARG C 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.824 Fit side-chains REVERT: A 166 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 248 ASN cc_start: 0.8041 (t0) cc_final: 0.7343 (m-40) REVERT: A 259 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 171 ASP cc_start: 0.8254 (t70) cc_final: 0.7998 (t70) REVERT: B 191 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8164 (mmtp) REVERT: C 188 LYS cc_start: 0.8095 (tttt) cc_final: 0.7830 (ttmm) REVERT: C 191 LYS cc_start: 0.8822 (tptt) cc_final: 0.8499 (tppt) REVERT: D 191 LYS cc_start: 0.8321 (mptt) cc_final: 0.7883 (mppt) outliers start: 18 outliers final: 17 residues processed: 115 average time/residue: 0.1531 time to fit residues: 25.5544 Evaluate side-chains 117 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 256 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 70.0000 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 0.0570 chunk 75 optimal weight: 20.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.182198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.177857 restraints weight = 11689.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.177406 restraints weight = 18766.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.177312 restraints weight = 23774.450| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7754 Z= 0.249 Angle : 0.447 5.986 10690 Z= 0.262 Chirality : 0.037 0.174 1418 Planarity : 0.002 0.013 1486 Dihedral : 3.903 22.571 1346 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.62 % Allowed : 28.93 % Favored : 65.45 % 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: 3.50 (0.23), residues: 1330 helix: 2.75 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -1.12 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 PHE 0.010 0.001 PHE A 205 TYR 0.010 0.001 TYR D 254 ARG 0.002 0.001 ARG D 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.49 seconds wall clock time: 30 minutes 54.87 seconds (1854.87 seconds total)