Starting phenix.real_space_refine (version: dev) on Thu May 12 19:30:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/05_2022/7p3r_13185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/05_2022/7p3r_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_13185/05_2022/7p3r_13185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/05_2022/7p3r_13185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/05_2022/7p3r_13185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3r_13185/05_2022/7p3r_13185.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4597/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: 4.81, per 1000 atoms: 0.62 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 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: 0.21 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: 2.42 Time building geometry restraints manager: 3.39 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 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. 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: 3.530 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: 20.300 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 26.630 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 % 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 *********************** 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 : 0.896 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1657 time to fit residues: 27.0036 Evaluate side-chains 91 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1618 ------------------------------------------------------------------------------- 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 182 ASN C 248 ASN C 249 GLN C 270 GLN D 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 7754 Z= 0.315 Angle : 0.510 5.493 10690 Z= 0.307 Chirality : 0.039 0.151 1418 Planarity : 0.003 0.017 1486 Dihedral : 4.857 23.376 1346 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.65 % 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: -0.48 (0.21), residues: 1330 helix: 0.09 (0.14), residues: 1148 sheet: None (None), residues: 0 loop : -2.22 (0.40), residues: 182 *********************** 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 118 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.1696 time to fit residues: 28.0587 Evaluate side-chains 103 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1250 time to fit residues: 2.3842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 40.0000 chunk 96 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7093 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 7754 Z= 0.380 Angle : 0.537 7.691 10690 Z= 0.318 Chirality : 0.041 0.210 1418 Planarity : 0.003 0.016 1486 Dihedral : 4.820 24.230 1346 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 5.34 % 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: 0.62 (0.22), residues: 1330 helix: 0.80 (0.14), residues: 1154 sheet: None (None), residues: 0 loop : -1.74 (0.44), residues: 176 *********************** 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 108 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.926 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 0.1631 time to fit residues: 24.1592 Evaluate side-chains 101 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0729 time to fit residues: 2.2247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 62 optimal weight: 50.0000 chunk 13 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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: 0.7063 moved from start: 0.2778 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= 0.243 Angle : 0.441 5.960 10690 Z= 0.263 Chirality : 0.037 0.169 1418 Planarity : 0.002 0.014 1486 Dihedral : 4.326 21.281 1346 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 3.37 % 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: 1.81 (0.22), residues: 1330 helix: 1.61 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.53 (0.46), residues: 168 *********************** 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 110 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.875 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.1632 time to fit residues: 24.8436 Evaluate side-chains 102 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1151 time to fit residues: 2.3976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 50.0000 chunk 88 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 50.0000 chunk 114 optimal weight: 6.9990 chunk 32 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 overall best weight: 2.2944 ------------------------------------------------------------------------------- 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: 0.7032 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7754 Z= 0.176 Angle : 0.413 6.669 10690 Z= 0.244 Chirality : 0.036 0.161 1418 Planarity : 0.002 0.014 1486 Dihedral : 4.025 20.263 1346 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.69 % 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: 2.64 (0.23), residues: 1330 helix: 2.16 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.39 (0.49), residues: 164 *********************** 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 106 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.886 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 103 average time/residue: 0.1743 time to fit residues: 25.7982 Evaluate side-chains 99 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0746 time to fit residues: 1.5186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 50.0000 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 D 259 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 7754 Z= 0.444 Angle : 0.577 10.899 10690 Z= 0.337 Chirality : 0.043 0.196 1418 Planarity : 0.003 0.015 1486 Dihedral : 4.762 26.314 1346 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.81 % 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: 1.60 (0.22), residues: 1330 helix: 1.48 (0.14), residues: 1158 sheet: None (None), residues: 0 loop : -1.62 (0.48), residues: 172 *********************** 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 104 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.868 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.1789 time to fit residues: 26.4576 Evaluate side-chains 95 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0726 time to fit residues: 1.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 40.0000 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7754 Z= 0.219 Angle : 0.442 6.048 10690 Z= 0.261 Chirality : 0.037 0.181 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.187 19.684 1346 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 2.53 % 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: 2.65 (0.23), residues: 1330 helix: 2.17 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.25 (0.51), residues: 170 *********************** 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 103 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.902 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 0.1694 time to fit residues: 24.3408 Evaluate side-chains 96 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0723 time to fit residues: 1.7079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7754 Z= 0.182 Angle : 0.428 5.898 10690 Z= 0.250 Chirality : 0.036 0.173 1418 Planarity : 0.002 0.015 1486 Dihedral : 3.887 19.885 1346 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.84 % 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: 3.28 (0.23), residues: 1330 helix: 2.61 (0.14), residues: 1164 sheet: None (None), residues: 0 loop : -1.28 (0.50), residues: 166 *********************** 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 103 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.848 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 102 average time/residue: 0.1532 time to fit residues: 22.8723 Evaluate side-chains 99 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0693 time to fit residues: 1.2597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 107 optimal weight: 0.4980 chunk 112 optimal weight: 50.0000 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7754 Z= 0.235 Angle : 0.457 6.135 10690 Z= 0.266 Chirality : 0.037 0.165 1418 Planarity : 0.002 0.014 1486 Dihedral : 3.974 20.862 1346 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.12 % 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: 3.28 (0.23), residues: 1330 helix: 2.57 (0.14), residues: 1167 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 163 *********************** 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 100 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.907 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 97 average time/residue: 0.1507 time to fit residues: 21.4285 Evaluate side-chains 100 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0762 time to fit residues: 1.5883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 131 optimal weight: 50.0000 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 80.0000 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 50.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7754 Z= 0.193 Angle : 0.437 5.923 10690 Z= 0.254 Chirality : 0.036 0.170 1418 Planarity : 0.002 0.016 1486 Dihedral : 3.828 19.543 1346 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.84 % 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: 3.62 (0.23), residues: 1330 helix: 2.81 (0.14), residues: 1166 sheet: None (None), residues: 0 loop : -1.02 (0.53), residues: 164 ********************** 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 100 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.875 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.1543 time to fit residues: 22.6171 Evaluate side-chains 97 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0710 time to fit residues: 1.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 70.0000 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 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 259 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.183680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.179442 restraints weight = 11627.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.179261 restraints weight = 20142.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.179131 restraints weight = 19322.194| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7754 Z= 0.212 Angle : 0.448 5.912 10690 Z= 0.260 Chirality : 0.037 0.168 1418 Planarity : 0.002 0.015 1486 Dihedral : 3.851 21.138 1346 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.56 % 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: 3.57 (0.23), residues: 1330 helix: 2.77 (0.14), residues: 1167 sheet: None (None), residues: 0 loop : -0.99 (0.54), residues: 163 =============================================================================== Job complete usr+sys time: 1451.72 seconds wall clock time: 26 minutes 49.50 seconds (1609.50 seconds total)