Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 12:31:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/07_2023/7tym_26185_neut.pdb" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7670 2.51 5 N 2160 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 832": "OE1" <-> "OE2" Residue "A TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 832": "OE1" <-> "OE2" Residue "B TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 12112 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6056 Classifications: {'peptide': 771} Link IDs: {'PTRANS': 40, 'TRANS': 730} Chain breaks: 7 Chain: "B" Number of atoms: 6056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6056 Classifications: {'peptide': 771} Link IDs: {'PTRANS': 40, 'TRANS': 730} Chain breaks: 7 Time building chain proxies: 6.05, per 1000 atoms: 0.50 Number of scatterers: 12112 At special positions: 0 Unit cell: (122.04, 154.44, 154.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2212 8.00 N 2160 7.00 C 7670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.04 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 838 " distance=2.03 Simple disulfide: pdb=" SG CYS A 764 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 232 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 1.8 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 11.2% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.510A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 19 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.831A pdb=" N ALA A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.580A pdb=" N CYS A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.636A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.916A pdb=" N GLY A 272 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.268A pdb=" N GLN A 316 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 319 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.806A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.136A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.899A pdb=" N PHE A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.510A pdb=" N GLN B 18 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.831A pdb=" N ALA B 138 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.581A pdb=" N CYS B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.637A pdb=" N CYS B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.915A pdb=" N GLY B 272 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.267A pdb=" N GLN B 316 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP B 317 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 318 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 319 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.806A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.136A pdb=" N ILE B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 693 Processing helix chain 'B' and resid 841 through 848 removed outlier: 3.899A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 8.186A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 9 removed outlier: 8.186A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU A 58 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 29 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 60 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 31 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL A 62 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 33 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG A 114 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 90 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU A 116 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 92 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 113 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.689A pdb=" N THR A 168 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP A 175 " --> pdb=" O THR A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 removed outlier: 3.551A pdb=" N ARG A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 309 removed outlier: 3.840A pdb=" N VAL A 304 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 327 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 306 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 329 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 308 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 3.840A pdb=" N VAL A 304 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 327 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 306 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 329 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 308 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS A 357 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 328 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS A 359 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 388 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 468 removed outlier: 6.581A pdb=" N ARG A 476 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN A 466 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 474 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR A 468 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 518 through 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 588 removed outlier: 5.669A pdb=" N ASP A 584 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 600 " --> pdb=" O ASP A 584 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 737 through 741 removed outlier: 3.567A pdb=" N VAL A 614 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 611 " --> pdb=" O CYS A 764 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 756 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 797 through 801 removed outlier: 3.848A pdb=" N SER A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 834 through 840 removed outlier: 3.650A pdb=" N TYR A 827 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 822 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 9 removed outlier: 8.185A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 5 through 9 removed outlier: 8.185A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LEU B 58 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 29 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 60 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 31 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL B 62 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU B 33 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 57 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE B 92 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 59 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG B 114 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 90 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLU B 116 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B 92 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 113 " --> pdb=" O HIS B 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.690A pdb=" N THR B 168 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP B 175 " --> pdb=" O THR B 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.552A pdb=" N ARG B 247 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 309 removed outlier: 3.839A pdb=" N VAL B 304 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 327 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 306 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 329 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 308 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 301 through 309 removed outlier: 3.839A pdb=" N VAL B 304 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 327 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 306 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 329 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 308 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS B 357 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 328 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS B 359 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 388 " --> pdb=" O TYR B 415 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.580A pdb=" N ARG B 476 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 466 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 474 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR B 468 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 518 through 522 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 588 removed outlier: 5.669A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.567A pdb=" N VAL B 614 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 797 through 801 removed outlier: 3.847A pdb=" N SER B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 834 through 840 removed outlier: 3.650A pdb=" N TYR B 827 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 822 " --> pdb=" O THR B 867 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 636 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: 4.32 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4034 1.35 - 1.48: 3074 1.48 - 1.60: 5204 1.60 - 1.73: 0 1.73 - 1.86: 80 Bond restraints: 12392 Sorted by residual: bond pdb=" CB CYS A 321 " pdb=" SG CYS A 321 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.20e+00 bond pdb=" CA THR B 553 " pdb=" CB THR B 553 " ideal model delta sigma weight residual 1.529 1.548 -0.019 1.58e-02 4.01e+03 1.40e+00 bond pdb=" CA THR A 553 " pdb=" CB THR A 553 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.58e-02 4.01e+03 1.34e+00 bond pdb=" C PRO A 237 " pdb=" N PRO A 238 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 ... (remaining 12387 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.20: 471 107.20 - 113.89: 6794 113.89 - 120.59: 4538 120.59 - 127.28: 4867 127.28 - 133.97: 164 Bond angle restraints: 16834 Sorted by residual: angle pdb=" CA CYS B 302 " pdb=" CB CYS B 302 " pdb=" SG CYS B 302 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" CA CYS A 302 " pdb=" CB CYS A 302 " pdb=" SG CYS A 302 " ideal model delta sigma weight residual 114.40 122.04 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA THR B 553 " pdb=" CB THR B 553 " pdb=" CG2 THR B 553 " ideal model delta sigma weight residual 110.50 114.63 -4.13 1.70e+00 3.46e-01 5.91e+00 angle pdb=" CA THR A 553 " pdb=" CB THR A 553 " pdb=" CG2 THR A 553 " ideal model delta sigma weight residual 110.50 114.63 -4.13 1.70e+00 3.46e-01 5.90e+00 angle pdb=" C PHE A 370 " pdb=" N LYS A 371 " pdb=" CA LYS A 371 " ideal model delta sigma weight residual 120.54 123.82 -3.28 1.35e+00 5.49e-01 5.89e+00 ... (remaining 16829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 6348 16.79 - 33.58: 816 33.58 - 50.38: 228 50.38 - 67.17: 36 67.17 - 83.96: 18 Dihedral angle restraints: 7446 sinusoidal: 3006 harmonic: 4440 Sorted by residual: dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 184 " pdb=" CB CYS B 184 " ideal model delta sinusoidal sigma weight residual 93.00 176.80 -83.80 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual 93.00 176.76 -83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -25.46 -60.54 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 7443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1394 0.041 - 0.082: 308 0.082 - 0.122: 160 0.122 - 0.163: 16 0.163 - 0.204: 2 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CA PHE B 418 " pdb=" N PHE B 418 " pdb=" C PHE B 418 " pdb=" CB PHE B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR A 553 " pdb=" CA THR A 553 " pdb=" OG1 THR A 553 " pdb=" CG2 THR A 553 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1877 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 778 " 0.013 2.00e-02 2.50e+03 1.69e-02 5.03e+00 pdb=" CG PHE B 778 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 778 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 778 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 778 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 778 " 0.012 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE A 778 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 778 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 778 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 778 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 778 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 778 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 418 " -0.023 2.00e-02 2.50e+03 1.52e-02 4.03e+00 pdb=" CG PHE B 418 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 418 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 418 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 418 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 418 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 418 " -0.014 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 454 2.72 - 3.27: 11367 3.27 - 3.81: 18708 3.81 - 4.36: 22710 4.36 - 4.90: 40028 Nonbonded interactions: 93267 Sorted by model distance: nonbonded pdb=" O GLY B 347 " pdb=" ND2 ASN B 372 " model vdw 2.175 2.520 nonbonded pdb=" O GLY A 347 " pdb=" ND2 ASN A 372 " model vdw 2.175 2.520 nonbonded pdb=" OG SER B 801 " pdb=" OG SER B 805 " model vdw 2.226 2.440 nonbonded pdb=" OG SER A 801 " pdb=" OG SER A 805 " model vdw 2.226 2.440 nonbonded pdb=" O LEU A 430 " pdb=" OG1 THR A 434 " model vdw 2.230 2.440 ... (remaining 93262 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 6.940 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.620 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 12392 Z= 0.152 Angle : 0.541 8.091 16834 Z= 0.280 Chirality : 0.043 0.204 1880 Planarity : 0.004 0.040 2176 Dihedral : 15.938 83.961 4502 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.78 % Rotamer Outliers : 0.00 % 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: -1.35 (0.22), residues: 1510 helix: 1.00 (0.53), residues: 112 sheet: -0.10 (0.26), residues: 376 loop : -1.52 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.428 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2560 time to fit residues: 30.5035 Evaluate side-chains 77 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 0.0370 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 12392 Z= 0.196 Angle : 0.511 5.752 16834 Z= 0.263 Chirality : 0.043 0.146 1880 Planarity : 0.004 0.040 2176 Dihedral : 4.240 24.237 1688 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 2.67 % 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: -1.39 (0.21), residues: 1510 helix: 1.05 (0.52), residues: 112 sheet: -0.06 (0.26), residues: 378 loop : -1.59 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 119 average time/residue: 0.2150 time to fit residues: 39.5738 Evaluate side-chains 93 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1167 time to fit residues: 5.1473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12392 Z= 0.199 Angle : 0.516 8.972 16834 Z= 0.264 Chirality : 0.043 0.167 1880 Planarity : 0.004 0.038 2176 Dihedral : 4.343 23.041 1688 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.91 % 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: -1.47 (0.21), residues: 1510 helix: 1.09 (0.52), residues: 112 sheet: -0.18 (0.26), residues: 378 loop : -1.64 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.458 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 108 average time/residue: 0.2493 time to fit residues: 39.8245 Evaluate side-chains 88 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1213 time to fit residues: 3.7289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN B 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 12392 Z= 0.234 Angle : 0.529 7.407 16834 Z= 0.271 Chirality : 0.044 0.181 1880 Planarity : 0.004 0.038 2176 Dihedral : 4.410 23.034 1688 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 1.37 % 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: -1.54 (0.21), residues: 1510 helix: 1.11 (0.52), residues: 112 sheet: -0.23 (0.26), residues: 380 loop : -1.69 (0.19), residues: 1018 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.388 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.2250 time to fit residues: 33.2210 Evaluate side-chains 84 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1074 time to fit residues: 4.4886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0460 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12392 Z= 0.215 Angle : 0.525 7.035 16834 Z= 0.268 Chirality : 0.043 0.183 1880 Planarity : 0.004 0.037 2176 Dihedral : 4.430 23.647 1688 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer Outliers : 0.91 % 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 (0.21), residues: 1510 helix: 1.09 (0.52), residues: 112 sheet: -0.32 (0.26), residues: 378 loop : -1.71 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.296 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.2715 time to fit residues: 33.9505 Evaluate side-chains 82 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1928 time to fit residues: 4.9013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 12392 Z= 0.406 Angle : 0.615 7.457 16834 Z= 0.317 Chirality : 0.046 0.195 1880 Planarity : 0.004 0.035 2176 Dihedral : 5.009 24.327 1688 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 1.60 % 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 (0.21), residues: 1510 helix: 1.31 (0.54), residues: 100 sheet: -0.52 (0.26), residues: 380 loop : -1.85 (0.19), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.438 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.2086 time to fit residues: 33.0596 Evaluate side-chains 90 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1100 time to fit residues: 4.3948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 617 GLN B 337 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12392 Z= 0.176 Angle : 0.536 6.831 16834 Z= 0.272 Chirality : 0.043 0.193 1880 Planarity : 0.004 0.036 2176 Dihedral : 4.597 24.460 1688 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 0.61 % 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: -1.69 (0.21), residues: 1510 helix: 1.38 (0.54), residues: 100 sheet: -0.48 (0.26), residues: 378 loop : -1.74 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.412 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 84 average time/residue: 0.2396 time to fit residues: 30.8064 Evaluate side-chains 84 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2774 time to fit residues: 3.0252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.0010 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 337 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 12392 Z= 0.384 Angle : 0.621 9.278 16834 Z= 0.317 Chirality : 0.046 0.207 1880 Planarity : 0.004 0.035 2176 Dihedral : 5.050 24.771 1688 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 1.22 % 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: -1.93 (0.21), residues: 1510 helix: 1.26 (0.55), residues: 100 sheet: -0.66 (0.25), residues: 380 loop : -1.92 (0.19), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.427 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.2173 time to fit residues: 32.1366 Evaluate side-chains 85 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1149 time to fit residues: 4.1960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 0.0020 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN B 337 ASN B 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 12392 Z= 0.163 Angle : 0.551 10.614 16834 Z= 0.280 Chirality : 0.044 0.204 1880 Planarity : 0.004 0.038 2176 Dihedral : 4.629 26.872 1688 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.23 % 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: -1.77 (0.21), residues: 1510 helix: 1.17 (0.55), residues: 100 sheet: -0.61 (0.25), residues: 388 loop : -1.75 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.502 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.2242 time to fit residues: 28.2333 Evaluate side-chains 73 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1059 time to fit residues: 2.2432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 617 GLN B 337 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 12392 Z= 0.295 Angle : 0.585 10.458 16834 Z= 0.297 Chirality : 0.045 0.197 1880 Planarity : 0.004 0.037 2176 Dihedral : 4.784 27.393 1688 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer Outliers : 0.30 % 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: -1.84 (0.21), residues: 1510 helix: 1.23 (0.56), residues: 100 sheet: -0.61 (0.25), residues: 378 loop : -1.83 (0.19), residues: 1032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.383 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.2306 time to fit residues: 26.8576 Evaluate side-chains 75 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1086 time to fit residues: 2.5051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098832 restraints weight = 18775.389| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.95 r_work: 0.3132 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12392 Z= 0.170 Angle : 0.541 10.931 16834 Z= 0.273 Chirality : 0.044 0.195 1880 Planarity : 0.004 0.038 2176 Dihedral : 4.549 29.600 1688 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 0.23 % 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: -1.76 (0.21), residues: 1510 helix: 0.79 (0.53), residues: 112 sheet: -0.48 (0.25), residues: 378 loop : -1.78 (0.19), residues: 1020 =============================================================================== Job complete usr+sys time: 2251.20 seconds wall clock time: 41 minutes 45.91 seconds (2505.91 seconds total)