Starting phenix.real_space_refine on Sun Mar 17 08:50:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sef_25067/03_2024/7sef_25067_neut.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 42 5.16 5 C 10848 2.51 5 N 2922 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 209": "NH1" <-> "NH2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17154 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Chain: "B" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Chain: "D" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Chain: "E" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Chain: "F" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Time building chain proxies: 9.17, per 1000 atoms: 0.53 Number of scatterers: 17154 At special positions: 0 Unit cell: (113.208, 114.48, 120.84, 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 42 16.00 O 3342 8.00 N 2922 7.00 C 10848 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: 6.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 24 sheets defined 12.0% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 209 through 215 removed outlier: 5.397A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 215 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.750A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 215 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.750A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'C' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 215 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.751A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 386' Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 215 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.751A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 333' Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'E' and resid 95 through 100 removed outlier: 4.029A pdb=" N ASP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 215 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.749A pdb=" N VAL E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 333' Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 95 through 100 removed outlier: 4.027A pdb=" N ASP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 209 through 215 removed outlier: 5.397A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 215 " --> pdb=" O THR F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.749A pdb=" N VAL F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE A 132 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 71 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE A 181 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 187 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 178 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE A 253 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 180 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 221 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 302 removed outlier: 3.568A pdb=" N GLY A 308 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 302 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 321 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 379 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 286 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 341 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 340 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 367 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 342 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE B 132 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 71 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 181 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 187 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 221 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY B 308 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR B 302 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 321 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 379 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 286 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 341 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 340 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 367 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 342 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 393 through 395 removed outlier: 5.968A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE C 132 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 71 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 161 through 167 removed outlier: 5.879A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE C 181 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 187 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 178 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE C 253 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR C 180 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 221 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY C 308 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 302 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL C 321 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL C 379 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 286 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 341 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 340 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 367 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 342 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE D 132 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 71 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE D 181 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 187 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 221 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 299 through 302 removed outlier: 3.566A pdb=" N GLY D 308 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR D 302 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU D 306 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 321 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 379 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 286 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 341 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 340 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 367 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 342 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE E 132 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL E 71 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 161 through 167 removed outlier: 5.879A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE E 181 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY E 187 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE E 221 " --> pdb=" O GLY E 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY E 308 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR E 302 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 321 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL E 379 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU E 286 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 341 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 340 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 367 " --> pdb=" O ARG E 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 342 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE F 132 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 71 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE F 181 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 187 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE F 221 " --> pdb=" O GLY F 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 299 through 302 removed outlier: 3.566A pdb=" N GLY F 308 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR F 302 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU F 306 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL F 321 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL F 379 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 286 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 341 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 340 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 367 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 342 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1116 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: 5.48 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5760 1.34 - 1.46: 2810 1.46 - 1.57: 8770 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 17424 Sorted by residual: bond pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 1.527 1.494 0.033 2.48e-02 1.63e+03 1.76e+00 bond pdb=" CA TYR C 68 " pdb=" CB TYR C 68 " ideal model delta sigma weight residual 1.527 1.495 0.033 2.48e-02 1.63e+03 1.73e+00 bond pdb=" CA TYR D 68 " pdb=" CB TYR D 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.72e+00 bond pdb=" CA TYR E 68 " pdb=" CB TYR E 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.67e+00 bond pdb=" CA TYR F 68 " pdb=" CB TYR F 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.67e+00 ... (remaining 17419 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.62: 454 105.62 - 112.69: 9599 112.69 - 119.77: 5408 119.77 - 126.84: 7951 126.84 - 133.91: 192 Bond angle restraints: 23604 Sorted by residual: angle pdb=" N SER A 297 " pdb=" CA SER A 297 " pdb=" C SER A 297 " ideal model delta sigma weight residual 114.56 111.01 3.55 1.27e+00 6.20e-01 7.82e+00 angle pdb=" N SER B 297 " pdb=" CA SER B 297 " pdb=" C SER B 297 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.75e+00 angle pdb=" CA VAL F 331 " pdb=" CB VAL F 331 " pdb=" CG1 VAL F 331 " ideal model delta sigma weight residual 110.40 114.33 -3.93 1.70e+00 3.46e-01 5.34e+00 angle pdb=" CA VAL E 331 " pdb=" CB VAL E 331 " pdb=" CG1 VAL E 331 " ideal model delta sigma weight residual 110.40 114.28 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" CA VAL C 331 " pdb=" CB VAL C 331 " pdb=" CG1 VAL C 331 " ideal model delta sigma weight residual 110.40 114.28 -3.88 1.70e+00 3.46e-01 5.21e+00 ... (remaining 23599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 10002 15.97 - 31.95: 486 31.95 - 47.92: 78 47.92 - 63.90: 42 63.90 - 79.87: 6 Dihedral angle restraints: 10614 sinusoidal: 4254 harmonic: 6360 Sorted by residual: dihedral pdb=" CA SER F 177 " pdb=" C SER F 177 " pdb=" N LEU F 178 " pdb=" CA LEU F 178 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER D 177 " pdb=" C SER D 177 " pdb=" N LEU D 178 " pdb=" CA LEU D 178 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER E 177 " pdb=" C SER E 177 " pdb=" N LEU E 178 " pdb=" CA LEU E 178 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 10611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1643 0.027 - 0.053: 608 0.053 - 0.080: 233 0.080 - 0.107: 206 0.107 - 0.133: 76 Chirality restraints: 2766 Sorted by residual: chirality pdb=" CA ILE F 203 " pdb=" N ILE F 203 " pdb=" C ILE F 203 " pdb=" CB ILE F 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE E 203 " pdb=" N ILE E 203 " pdb=" C ILE E 203 " pdb=" CB ILE E 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2763 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 331 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C VAL C 331 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 331 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 332 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 331 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C VAL F 331 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL F 331 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL F 332 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 331 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C VAL A 331 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL A 331 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 332 " -0.008 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4302 2.79 - 3.32: 16263 3.32 - 3.85: 26822 3.85 - 4.37: 31382 4.37 - 4.90: 54084 Nonbonded interactions: 132853 Sorted by model distance: nonbonded pdb=" NH1 ARG C 340 " pdb=" O ALA C 385 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG E 340 " pdb=" O ALA E 385 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG A 340 " pdb=" O ALA A 385 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG D 340 " pdb=" O ALA D 385 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG B 340 " pdb=" O ALA B 385 " model vdw 2.267 2.520 ... (remaining 132848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 14.070 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 45.020 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.005 0.033 17424 Z= 0.354 Angle : 0.672 5.352 23604 Z= 0.359 Chirality : 0.043 0.133 2766 Planarity : 0.003 0.030 3072 Dihedral : 10.539 79.872 6534 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2208 helix: -2.44 (0.29), residues: 192 sheet: -0.78 (0.17), residues: 666 loop : -1.54 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 109 HIS 0.002 0.001 HIS B 388 PHE 0.005 0.001 PHE A 253 TYR 0.016 0.002 TYR D 131 ARG 0.003 0.001 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8401 (tpt) cc_final: 0.8116 (tpt) REVERT: B 162 MET cc_start: 0.8147 (tpt) cc_final: 0.7726 (tpt) REVERT: C 54 MET cc_start: 0.8951 (mmp) cc_final: 0.8644 (mmp) REVERT: C 162 MET cc_start: 0.8156 (tpt) cc_final: 0.7771 (tpt) REVERT: D 301 MET cc_start: 0.8997 (mmp) cc_final: 0.8139 (mmm) REVERT: E 63 ARG cc_start: 0.9037 (ptt90) cc_final: 0.8824 (tmm160) REVERT: E 301 MET cc_start: 0.9196 (mmp) cc_final: 0.8767 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3731 time to fit residues: 32.0861 Evaluate side-chains 45 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 89 optimal weight: 0.2980 chunk 174 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 0.1980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.8405 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17424 Z= 0.144 Angle : 0.551 8.508 23604 Z= 0.280 Chirality : 0.044 0.151 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.551 16.650 2376 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.53 % Allowed : 6.07 % Favored : 93.41 % 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: -1.72 (0.16), residues: 2208 helix: -1.09 (0.35), residues: 198 sheet: -0.35 (0.18), residues: 654 loop : -1.60 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 222 HIS 0.002 0.000 HIS F 144 PHE 0.010 0.001 PHE F 221 TYR 0.010 0.001 TYR E 154 ARG 0.006 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 2.272 Fit side-chains REVERT: A 162 MET cc_start: 0.8383 (tpt) cc_final: 0.8071 (tpt) REVERT: B 162 MET cc_start: 0.8119 (tpt) cc_final: 0.7835 (tpt) REVERT: C 54 MET cc_start: 0.8849 (mmp) cc_final: 0.8585 (mmp) REVERT: C 162 MET cc_start: 0.8099 (tpt) cc_final: 0.7780 (tpt) REVERT: C 301 MET cc_start: 0.8374 (mmm) cc_final: 0.8039 (mmm) REVERT: D 301 MET cc_start: 0.8861 (mmp) cc_final: 0.8155 (mmm) REVERT: E 135 MET cc_start: 0.8563 (ppp) cc_final: 0.8355 (ppp) REVERT: E 301 MET cc_start: 0.8982 (mmp) cc_final: 0.8717 (mmm) outliers start: 10 outliers final: 2 residues processed: 56 average time/residue: 0.3196 time to fit residues: 29.5194 Evaluate side-chains 44 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 440 GLN C 440 GLN D 130 ASN D 440 GLN E 130 ASN E 440 GLN F 130 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17424 Z= 0.287 Angle : 0.631 7.870 23604 Z= 0.318 Chirality : 0.044 0.154 2766 Planarity : 0.004 0.029 3072 Dihedral : 4.739 17.626 2376 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.16 % Allowed : 5.43 % Favored : 92.41 % 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: -1.75 (0.17), residues: 2208 helix: -0.68 (0.37), residues: 210 sheet: -0.56 (0.19), residues: 684 loop : -1.61 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 222 HIS 0.003 0.001 HIS B 144 PHE 0.014 0.002 PHE F 221 TYR 0.010 0.001 TYR B 131 ARG 0.007 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 42 time to evaluate : 2.158 Fit side-chains REVERT: A 54 MET cc_start: 0.8422 (mpp) cc_final: 0.7833 (tpp) REVERT: A 120 VAL cc_start: 0.5755 (OUTLIER) cc_final: 0.5405 (t) REVERT: B 120 VAL cc_start: 0.4315 (OUTLIER) cc_final: 0.4038 (t) REVERT: B 134 MET cc_start: 0.9053 (ppp) cc_final: 0.8850 (ppp) REVERT: B 162 MET cc_start: 0.8612 (tpt) cc_final: 0.8406 (tpp) REVERT: B 301 MET cc_start: 0.9132 (mmm) cc_final: 0.8686 (mmm) REVERT: B 354 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8337 (p0) REVERT: C 54 MET cc_start: 0.8475 (mmp) cc_final: 0.8258 (mpp) REVERT: C 162 MET cc_start: 0.8673 (tpt) cc_final: 0.8444 (tpp) REVERT: D 120 VAL cc_start: 0.6434 (OUTLIER) cc_final: 0.6128 (t) REVERT: D 162 MET cc_start: 0.8749 (tpp) cc_final: 0.8435 (tpp) REVERT: D 301 MET cc_start: 0.9191 (mmp) cc_final: 0.8733 (mmm) REVERT: E 120 VAL cc_start: 0.5104 (OUTLIER) cc_final: 0.4864 (t) REVERT: E 301 MET cc_start: 0.9244 (mmp) cc_final: 0.9034 (mmm) outliers start: 41 outliers final: 6 residues processed: 83 average time/residue: 0.2095 time to fit residues: 31.3485 Evaluate side-chains 53 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17424 Z= 0.237 Angle : 0.578 9.711 23604 Z= 0.290 Chirality : 0.044 0.147 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.550 17.381 2376 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 6.07 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2208 helix: 0.94 (0.41), residues: 162 sheet: -0.51 (0.18), residues: 696 loop : -1.48 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS D 441 PHE 0.009 0.001 PHE F 221 TYR 0.010 0.001 TYR C 131 ARG 0.002 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 42 time to evaluate : 2.263 Fit side-chains REVERT: A 54 MET cc_start: 0.8328 (mpp) cc_final: 0.7844 (tpp) REVERT: A 120 VAL cc_start: 0.6003 (OUTLIER) cc_final: 0.5678 (t) REVERT: A 162 MET cc_start: 0.8693 (tpp) cc_final: 0.8450 (tpp) REVERT: A 301 MET cc_start: 0.8833 (mmp) cc_final: 0.8284 (mmm) REVERT: B 120 VAL cc_start: 0.4405 (OUTLIER) cc_final: 0.4122 (t) REVERT: B 162 MET cc_start: 0.8717 (tpt) cc_final: 0.8474 (tpp) REVERT: B 301 MET cc_start: 0.9122 (mmm) cc_final: 0.8612 (mmm) REVERT: C 134 MET cc_start: 0.9162 (ppp) cc_final: 0.8930 (ppp) REVERT: C 162 MET cc_start: 0.8789 (tpt) cc_final: 0.8512 (tpp) REVERT: D 120 VAL cc_start: 0.6503 (OUTLIER) cc_final: 0.6213 (t) REVERT: D 162 MET cc_start: 0.8541 (tpp) cc_final: 0.8138 (tpp) REVERT: D 301 MET cc_start: 0.9140 (mmp) cc_final: 0.8819 (mmm) REVERT: E 120 VAL cc_start: 0.5282 (OUTLIER) cc_final: 0.5022 (t) REVERT: F 162 MET cc_start: 0.8341 (tmm) cc_final: 0.8129 (tpp) outliers start: 32 outliers final: 12 residues processed: 73 average time/residue: 0.2226 time to fit residues: 29.2897 Evaluate side-chains 58 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 7.9990 chunk 121 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 17424 Z= 0.448 Angle : 0.750 12.159 23604 Z= 0.368 Chirality : 0.045 0.161 2766 Planarity : 0.004 0.030 3072 Dihedral : 5.196 21.356 2376 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.90 % Allowed : 6.38 % Favored : 91.72 % 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: -1.79 (0.17), residues: 2208 helix: -0.99 (0.34), residues: 210 sheet: -0.52 (0.19), residues: 696 loop : -1.64 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 222 HIS 0.007 0.001 HIS A 441 PHE 0.013 0.002 PHE C 53 TYR 0.012 0.002 TYR B 131 ARG 0.004 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 42 time to evaluate : 2.110 Fit side-chains REVERT: A 54 MET cc_start: 0.8224 (mpp) cc_final: 0.7827 (tpp) REVERT: A 81 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 120 VAL cc_start: 0.6787 (OUTLIER) cc_final: 0.6561 (t) REVERT: A 162 MET cc_start: 0.8293 (tpp) cc_final: 0.7916 (tpp) REVERT: B 73 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8737 (m) REVERT: B 120 VAL cc_start: 0.5419 (OUTLIER) cc_final: 0.5104 (t) REVERT: B 162 MET cc_start: 0.8785 (tpt) cc_final: 0.8461 (tpp) REVERT: B 301 MET cc_start: 0.9273 (mmm) cc_final: 0.8830 (mmm) REVERT: C 162 MET cc_start: 0.8908 (tpt) cc_final: 0.8584 (tpp) REVERT: D 54 MET cc_start: 0.8322 (mpp) cc_final: 0.8040 (mmp) REVERT: D 81 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8159 (tp) REVERT: D 120 VAL cc_start: 0.6575 (OUTLIER) cc_final: 0.6372 (t) REVERT: D 134 MET cc_start: 0.9167 (ppp) cc_final: 0.8876 (ppp) REVERT: D 162 MET cc_start: 0.8548 (tpp) cc_final: 0.8066 (tpp) REVERT: D 301 MET cc_start: 0.9316 (mmp) cc_final: 0.9001 (mmm) REVERT: E 120 VAL cc_start: 0.5726 (OUTLIER) cc_final: 0.5512 (t) outliers start: 36 outliers final: 16 residues processed: 75 average time/residue: 0.2290 time to fit residues: 30.2834 Evaluate side-chains 65 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 0.0870 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN E 130 ASN E 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17424 Z= 0.136 Angle : 0.556 10.259 23604 Z= 0.273 Chirality : 0.044 0.160 2766 Planarity : 0.003 0.030 3072 Dihedral : 4.467 16.405 2376 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 7.33 % Favored : 91.46 % 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: -1.51 (0.17), residues: 2208 helix: -0.60 (0.41), residues: 174 sheet: -0.50 (0.18), residues: 714 loop : -1.36 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 222 HIS 0.004 0.001 HIS F 441 PHE 0.009 0.001 PHE D 53 TYR 0.010 0.001 TYR B 131 ARG 0.002 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 2.127 Fit side-chains REVERT: A 54 MET cc_start: 0.8156 (mpp) cc_final: 0.7782 (tpp) REVERT: A 120 VAL cc_start: 0.6752 (OUTLIER) cc_final: 0.6517 (t) REVERT: A 162 MET cc_start: 0.8374 (tpp) cc_final: 0.8109 (tpp) REVERT: B 98 MET cc_start: 0.8724 (pmm) cc_final: 0.8510 (pmm) REVERT: B 120 VAL cc_start: 0.5117 (OUTLIER) cc_final: 0.4811 (t) REVERT: B 162 MET cc_start: 0.8829 (tpt) cc_final: 0.8550 (tpp) REVERT: B 301 MET cc_start: 0.9209 (mmm) cc_final: 0.8774 (mmm) REVERT: C 81 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8136 (tp) REVERT: C 162 MET cc_start: 0.8982 (tpt) cc_final: 0.8743 (tpp) REVERT: D 120 VAL cc_start: 0.6402 (OUTLIER) cc_final: 0.6160 (t) REVERT: D 134 MET cc_start: 0.9202 (ppp) cc_final: 0.8896 (ppp) REVERT: D 162 MET cc_start: 0.8339 (tpp) cc_final: 0.7927 (tpp) REVERT: E 81 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8549 (tp) REVERT: E 120 VAL cc_start: 0.5598 (OUTLIER) cc_final: 0.5341 (t) REVERT: E 135 MET cc_start: 0.8794 (ppp) cc_final: 0.8383 (ppp) outliers start: 23 outliers final: 11 residues processed: 64 average time/residue: 0.2302 time to fit residues: 26.4382 Evaluate side-chains 59 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17424 Z= 0.301 Angle : 0.619 9.947 23604 Z= 0.302 Chirality : 0.044 0.154 2766 Planarity : 0.003 0.031 3072 Dihedral : 4.584 17.289 2376 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.53 % Allowed : 7.81 % Favored : 90.66 % 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: -1.45 (0.17), residues: 2208 helix: -0.65 (0.40), residues: 174 sheet: -0.39 (0.19), residues: 690 loop : -1.34 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 222 HIS 0.004 0.001 HIS D 441 PHE 0.008 0.001 PHE F 221 TYR 0.009 0.001 TYR B 131 ARG 0.002 0.000 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 1.955 Fit side-chains REVERT: A 120 VAL cc_start: 0.6882 (OUTLIER) cc_final: 0.6636 (t) REVERT: A 162 MET cc_start: 0.8361 (tpp) cc_final: 0.8028 (tpp) REVERT: B 81 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7863 (tp) REVERT: B 120 VAL cc_start: 0.5518 (OUTLIER) cc_final: 0.5207 (t) REVERT: B 134 MET cc_start: 0.9027 (ppp) cc_final: 0.8827 (ppp) REVERT: B 162 MET cc_start: 0.8792 (tpt) cc_final: 0.8480 (tpp) REVERT: B 301 MET cc_start: 0.9255 (mmm) cc_final: 0.8798 (mmm) REVERT: C 81 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8146 (tp) REVERT: C 98 MET cc_start: 0.9081 (pmm) cc_final: 0.8875 (pmm) REVERT: C 162 MET cc_start: 0.8938 (tpt) cc_final: 0.8629 (tpp) REVERT: D 54 MET cc_start: 0.8131 (mmp) cc_final: 0.7913 (mpp) REVERT: D 81 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 120 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6371 (t) REVERT: D 134 MET cc_start: 0.9259 (ppp) cc_final: 0.8953 (ppp) REVERT: D 162 MET cc_start: 0.8429 (tpp) cc_final: 0.7955 (tpp) REVERT: E 120 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5536 (t) REVERT: F 81 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8528 (tp) REVERT: F 98 MET cc_start: 0.8868 (mtm) cc_final: 0.8479 (pmm) outliers start: 29 outliers final: 15 residues processed: 70 average time/residue: 0.2392 time to fit residues: 29.4533 Evaluate side-chains 65 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17424 Z= 0.209 Angle : 0.583 11.956 23604 Z= 0.282 Chirality : 0.044 0.155 2766 Planarity : 0.003 0.030 3072 Dihedral : 4.411 16.387 2376 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.53 % Allowed : 8.02 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2208 helix: -0.57 (0.41), residues: 174 sheet: -0.34 (0.19), residues: 702 loop : -1.34 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 222 HIS 0.004 0.001 HIS F 441 PHE 0.008 0.001 PHE C 53 TYR 0.008 0.001 TYR B 131 ARG 0.001 0.000 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 2.121 Fit side-chains REVERT: A 54 MET cc_start: 0.7953 (mmp) cc_final: 0.7751 (mpp) REVERT: A 81 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8057 (tp) REVERT: A 120 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6689 (t) REVERT: A 162 MET cc_start: 0.8302 (tpp) cc_final: 0.7987 (tpp) REVERT: B 81 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 120 VAL cc_start: 0.5494 (OUTLIER) cc_final: 0.5182 (t) REVERT: B 162 MET cc_start: 0.8798 (tpt) cc_final: 0.8484 (tpp) REVERT: B 301 MET cc_start: 0.9213 (mmm) cc_final: 0.8785 (mmm) REVERT: C 81 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8158 (tp) REVERT: C 162 MET cc_start: 0.8949 (tpt) cc_final: 0.8707 (tpp) REVERT: D 54 MET cc_start: 0.8083 (mmp) cc_final: 0.7867 (mpp) REVERT: D 81 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 120 VAL cc_start: 0.6675 (OUTLIER) cc_final: 0.6448 (t) REVERT: D 134 MET cc_start: 0.9283 (ppp) cc_final: 0.9012 (ppp) REVERT: D 162 MET cc_start: 0.8401 (tpp) cc_final: 0.7958 (tpp) REVERT: E 120 VAL cc_start: 0.5734 (OUTLIER) cc_final: 0.5464 (t) outliers start: 29 outliers final: 16 residues processed: 69 average time/residue: 0.2359 time to fit residues: 29.2477 Evaluate side-chains 66 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 198 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17424 Z= 0.349 Angle : 0.671 12.723 23604 Z= 0.326 Chirality : 0.044 0.151 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.733 18.160 2376 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.42 % Allowed : 8.23 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2208 helix: -0.76 (0.39), residues: 174 sheet: -0.41 (0.19), residues: 702 loop : -1.38 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 222 HIS 0.005 0.001 HIS F 441 PHE 0.009 0.002 PHE F 433 TYR 0.009 0.001 TYR B 131 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7934 (mmp) cc_final: 0.7702 (mpp) REVERT: A 81 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 120 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6718 (t) REVERT: A 162 MET cc_start: 0.8308 (tpp) cc_final: 0.8052 (tpp) REVERT: B 81 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7927 (tp) REVERT: B 120 VAL cc_start: 0.5891 (OUTLIER) cc_final: 0.5593 (t) REVERT: B 162 MET cc_start: 0.8797 (tpt) cc_final: 0.8499 (tpp) REVERT: B 301 MET cc_start: 0.9250 (mmm) cc_final: 0.8820 (mmm) REVERT: C 81 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8278 (tp) REVERT: C 98 MET cc_start: 0.8932 (pmm) cc_final: 0.8692 (pmm) REVERT: C 162 MET cc_start: 0.8930 (tpt) cc_final: 0.8623 (tpp) REVERT: D 54 MET cc_start: 0.8035 (mmp) cc_final: 0.7828 (mpp) REVERT: D 81 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8199 (tp) REVERT: D 134 MET cc_start: 0.9313 (ppp) cc_final: 0.9016 (ppp) REVERT: D 162 MET cc_start: 0.8472 (tpp) cc_final: 0.7953 (tpp) REVERT: E 120 VAL cc_start: 0.5943 (OUTLIER) cc_final: 0.5698 (t) outliers start: 27 outliers final: 17 residues processed: 67 average time/residue: 0.2320 time to fit residues: 27.3403 Evaluate side-chains 66 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 176 optimal weight: 0.0770 chunk 18 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN F 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17424 Z= 0.176 Angle : 0.586 12.916 23604 Z= 0.283 Chirality : 0.044 0.157 2766 Planarity : 0.003 0.033 3072 Dihedral : 4.350 15.640 2376 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.05 % Allowed : 8.54 % Favored : 90.40 % 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: -1.17 (0.17), residues: 2208 helix: 1.33 (0.47), residues: 126 sheet: 0.04 (0.20), residues: 612 loop : -1.41 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.004 0.001 HIS F 441 PHE 0.008 0.001 PHE D 53 TYR 0.008 0.001 TYR B 131 ARG 0.002 0.000 ARG B 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7940 (mmp) cc_final: 0.7708 (mpp) REVERT: A 120 VAL cc_start: 0.6646 (OUTLIER) cc_final: 0.6416 (t) REVERT: A 134 MET cc_start: 0.9128 (ppp) cc_final: 0.8707 (ppp) REVERT: B 81 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 120 VAL cc_start: 0.5772 (OUTLIER) cc_final: 0.5470 (t) REVERT: B 162 MET cc_start: 0.8741 (tpt) cc_final: 0.8450 (tpp) REVERT: B 301 MET cc_start: 0.9222 (mmm) cc_final: 0.8793 (mmm) REVERT: C 81 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8276 (tp) REVERT: C 98 MET cc_start: 0.8897 (pmm) cc_final: 0.8627 (pmm) REVERT: C 162 MET cc_start: 0.8879 (tpt) cc_final: 0.8615 (tpp) REVERT: D 54 MET cc_start: 0.7953 (mmp) cc_final: 0.7732 (mpp) REVERT: D 162 MET cc_start: 0.8379 (tpp) cc_final: 0.7953 (tpp) REVERT: E 120 VAL cc_start: 0.5815 (OUTLIER) cc_final: 0.5536 (t) REVERT: F 135 MET cc_start: 0.8843 (ppp) cc_final: 0.8483 (ppp) outliers start: 20 outliers final: 13 residues processed: 62 average time/residue: 0.2364 time to fit residues: 26.3715 Evaluate side-chains 60 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 204 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 176 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 181 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 354 ASN B 440 GLN D 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.036340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027496 restraints weight = 145289.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.028354 restraints weight = 79922.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.028912 restraints weight = 53667.497| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17424 Z= 0.170 Angle : 0.592 12.920 23604 Z= 0.281 Chirality : 0.044 0.156 2766 Planarity : 0.003 0.039 3072 Dihedral : 4.178 15.068 2376 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.05 % Allowed : 8.81 % Favored : 90.14 % 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: -1.06 (0.17), residues: 2208 helix: 1.53 (0.49), residues: 126 sheet: 0.11 (0.20), residues: 600 loop : -1.32 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.003 0.001 HIS F 441 PHE 0.008 0.001 PHE D 145 TYR 0.007 0.001 TYR D 68 ARG 0.001 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.36 seconds wall clock time: 44 minutes 57.53 seconds (2697.53 seconds total)