Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:45:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/02_2023/7uwq_26838.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.108 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 Process input model Symmetric amino acids flipped Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 332": "OD1" <-> "OD2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C ASP 332": "OD1" <-> "OD2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 290": "OD1" <-> "OD2" Residue "E ASP 332": "OD1" <-> "OD2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 290": "OD1" <-> "OD2" Residue "F ASP 332": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Chain: "C" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Chain: "D" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Chain: "E" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Chain: "F" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Time building chain proxies: 11.64, per 1000 atoms: 0.57 Number of scatterers: 20538 At special positions: 0 Unit cell: (143.145, 133.365, 118.25, 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 66 16.00 O 3846 8.00 N 3528 7.00 C 13098 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: 7.26 Conformation dependent library (CDL) restraints added in 2.6 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 41.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.551A pdb=" N LEU A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.747A pdb=" N PHE A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.880A pdb=" N THR A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 344 through 360 removed outlier: 3.550A pdb=" N GLY A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.552A pdb=" N LEU B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.747A pdb=" N PHE B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.550A pdb=" N GLY B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 385 Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.736A pdb=" N GLY B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 466 removed outlier: 3.615A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.552A pdb=" N LEU C 104 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.749A pdb=" N PHE C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL C 210 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 222 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.645A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 344 through 360 removed outlier: 3.548A pdb=" N GLY C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 385 Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY C 433 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA D 13 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.551A pdb=" N LEU D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 4.138A pdb=" N ILE D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.901A pdb=" N VAL D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 222 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 3.879A pdb=" N THR D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 288 " --> pdb=" O ASN D 284 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 344 through 360 removed outlier: 3.549A pdb=" N GLY D 360 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 Processing helix chain 'D' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG D 393 " --> pdb=" O ALA D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY D 433 " --> pdb=" O PRO D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 466 removed outlier: 3.615A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA E 13 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 removed outlier: 3.553A pdb=" N LEU E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.137A pdb=" N ILE E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 184 " --> pdb=" O ASP E 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 185 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 222 removed outlier: 3.903A pdb=" N VAL E 210 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 222 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 344 through 360 removed outlier: 3.548A pdb=" N GLY E 360 " --> pdb=" O LYS E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 Processing helix chain 'E' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG E 393 " --> pdb=" O ALA E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.738A pdb=" N GLY E 433 " --> pdb=" O PRO E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 39 removed outlier: 3.514A pdb=" N ALA F 13 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.553A pdb=" N LEU F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 185 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 222 " --> pdb=" O CYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.645A pdb=" N LYS F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 293 removed outlier: 3.880A pdb=" N THR F 287 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 288 " --> pdb=" O ASN F 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 344 through 360 removed outlier: 3.549A pdb=" N GLY F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 Processing helix chain 'F' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG F 393 " --> pdb=" O ALA F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 416 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY F 433 " --> pdb=" O PRO F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 86 removed outlier: 5.131A pdb=" N TYR A 54 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE A 237 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 230 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 273 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 200 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 276 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 202 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU A 423 " --> pdb=" O TRP A 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET A 302 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS A 425 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 304 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER A 427 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS A 306 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 375 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 324 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR A 377 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG A 326 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 400 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR A 374 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 402 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 376 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR B 54 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.700A pdb=" N ILE B 237 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 230 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 273 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR B 200 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 276 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 202 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU B 423 " --> pdb=" O TRP B 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET B 302 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS B 425 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 304 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER B 427 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS B 306 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL B 375 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR B 324 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 377 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG B 326 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 400 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR B 374 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 402 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 376 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR C 54 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.701A pdb=" N ILE C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 230 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 273 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR C 200 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE C 276 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 202 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU C 423 " --> pdb=" O TRP C 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET C 302 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS C 425 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 304 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER C 427 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N CYS C 306 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 375 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 324 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 377 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG C 326 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL C 400 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR C 374 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 402 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 376 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR D 54 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.701A pdb=" N ILE D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 230 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 273 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR D 200 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 276 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 202 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU D 423 " --> pdb=" O TRP D 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET D 302 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS D 425 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 304 " --> pdb=" O CYS D 425 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER D 427 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS D 306 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 375 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR D 324 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR D 377 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG D 326 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL D 400 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR D 374 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE D 402 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 376 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR E 54 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE E 237 " --> pdb=" O CYS E 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 230 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 273 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR E 200 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE E 276 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 202 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU E 423 " --> pdb=" O TRP E 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET E 302 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS E 425 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY E 304 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER E 427 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS E 306 " --> pdb=" O SER E 427 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL E 375 " --> pdb=" O HIS E 322 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR E 324 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR E 377 " --> pdb=" O TYR E 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG E 326 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL E 400 " --> pdb=" O THR E 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR E 374 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE E 402 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 376 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 82 through 86 removed outlier: 5.131A pdb=" N TYR F 54 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE F 237 " --> pdb=" O CYS F 233 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 230 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 273 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR F 200 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE F 276 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 202 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU F 423 " --> pdb=" O TRP F 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 302 " --> pdb=" O LEU F 423 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS F 425 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY F 304 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER F 427 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS F 306 " --> pdb=" O SER F 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL F 375 " --> pdb=" O HIS F 322 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR F 324 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR F 377 " --> pdb=" O TYR F 324 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG F 326 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 400 " --> pdb=" O THR F 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR F 374 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE F 402 " --> pdb=" O THR F 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 376 " --> pdb=" O ILE F 402 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2358 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: 6.42 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6763 1.34 - 1.46: 3896 1.46 - 1.57: 10293 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 21048 Sorted by residual: bond pdb=" CB THR A 190 " pdb=" CG2 THR A 190 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.05e-01 bond pdb=" CB THR B 190 " pdb=" CG2 THR B 190 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR C 190 " pdb=" CG2 THR C 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.72e-01 bond pdb=" CB THR E 190 " pdb=" CG2 THR E 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 bond pdb=" CB THR D 190 " pdb=" CG2 THR D 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 750 106.98 - 113.74: 11676 113.74 - 120.49: 8410 120.49 - 127.24: 7562 127.24 - 133.99: 288 Bond angle restraints: 28686 Sorted by residual: angle pdb=" N TYR D 123 " pdb=" CA TYR D 123 " pdb=" C TYR D 123 " ideal model delta sigma weight residual 109.81 114.62 -4.81 2.21e+00 2.05e-01 4.74e+00 angle pdb=" N TYR C 123 " pdb=" CA TYR C 123 " pdb=" C TYR C 123 " ideal model delta sigma weight residual 109.81 114.56 -4.75 2.21e+00 2.05e-01 4.62e+00 angle pdb=" N TYR F 123 " pdb=" CA TYR F 123 " pdb=" C TYR F 123 " ideal model delta sigma weight residual 109.81 114.51 -4.70 2.21e+00 2.05e-01 4.51e+00 angle pdb=" N TYR E 123 " pdb=" CA TYR E 123 " pdb=" C TYR E 123 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.51e+00 angle pdb=" N TYR A 123 " pdb=" CA TYR A 123 " pdb=" C TYR A 123 " ideal model delta sigma weight residual 109.81 114.48 -4.67 2.21e+00 2.05e-01 4.47e+00 ... (remaining 28681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 11192 17.26 - 34.52: 1021 34.52 - 51.78: 201 51.78 - 69.05: 30 69.05 - 86.31: 18 Dihedral angle restraints: 12462 sinusoidal: 4896 harmonic: 7566 Sorted by residual: dihedral pdb=" CA LYS A 256 " pdb=" C LYS A 256 " pdb=" N LYS A 257 " pdb=" CA LYS A 257 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LYS C 256 " pdb=" C LYS C 256 " pdb=" N LYS C 257 " pdb=" CA LYS C 257 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LYS E 256 " pdb=" C LYS E 256 " pdb=" N LYS E 257 " pdb=" CA LYS E 257 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 12459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2002 0.036 - 0.072: 890 0.072 - 0.108: 216 0.108 - 0.144: 87 0.144 - 0.181: 9 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE E 250 " pdb=" CA ILE E 250 " pdb=" CG1 ILE E 250 " pdb=" CG2 ILE E 250 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB ILE F 250 " pdb=" CA ILE F 250 " pdb=" CG1 ILE F 250 " pdb=" CG2 ILE F 250 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 3201 not shown) Planarity restraints: 3702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 245 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 246 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 245 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO F 246 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 246 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 246 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 245 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 246 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 246 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 246 " -0.030 5.00e-02 4.00e+02 ... (remaining 3699 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6524 2.83 - 3.35: 16777 3.35 - 3.87: 30583 3.87 - 4.38: 34200 4.38 - 4.90: 64111 Nonbonded interactions: 152195 Sorted by model distance: nonbonded pdb=" OE1 GLU A 150 " pdb=" NE2 GLN A 153 " model vdw 2.313 2.520 nonbonded pdb=" OE1 GLU D 150 " pdb=" NE2 GLN D 153 " model vdw 2.313 2.520 nonbonded pdb=" OE1 GLU B 150 " pdb=" NE2 GLN B 153 " model vdw 2.313 2.520 nonbonded pdb=" OE1 GLU E 150 " pdb=" NE2 GLN E 153 " model vdw 2.313 2.520 nonbonded pdb=" OE1 GLU C 150 " pdb=" NE2 GLN C 153 " model vdw 2.313 2.520 ... (remaining 152190 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 13098 2.51 5 N 3528 2.21 5 O 3846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.030 Extract box with map and model: 11.710 Check model and map are aligned: 0.270 Process input model: 49.970 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 0.038 21048 Z= 0.303 Angle : 0.574 6.821 28686 Z= 0.323 Chirality : 0.044 0.181 3204 Planarity : 0.005 0.055 3702 Dihedral : 13.810 86.306 7602 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2538 helix: 0.21 (0.17), residues: 1032 sheet: 0.50 (0.24), residues: 468 loop : -1.47 (0.19), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3853 time to fit residues: 131.1642 Evaluate side-chains 185 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8537 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.148 Angle : 0.473 6.074 28686 Z= 0.247 Chirality : 0.041 0.141 3204 Planarity : 0.004 0.040 3702 Dihedral : 3.920 26.592 2874 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2538 helix: 0.59 (0.17), residues: 1038 sheet: 0.80 (0.25), residues: 468 loop : -1.22 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 2.684 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 207 average time/residue: 0.3502 time to fit residues: 110.6217 Evaluate side-chains 188 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1884 time to fit residues: 6.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21048 Z= 0.233 Angle : 0.498 6.164 28686 Z= 0.259 Chirality : 0.042 0.139 3204 Planarity : 0.004 0.042 3702 Dihedral : 3.901 26.982 2874 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2538 helix: 0.55 (0.17), residues: 1068 sheet: 0.70 (0.25), residues: 468 loop : -1.20 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 2.318 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 209 average time/residue: 0.3490 time to fit residues: 111.6865 Evaluate side-chains 193 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1796 time to fit residues: 8.0019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN E 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 21048 Z= 0.173 Angle : 0.458 6.117 28686 Z= 0.239 Chirality : 0.041 0.136 3204 Planarity : 0.004 0.048 3702 Dihedral : 3.709 26.773 2874 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2538 helix: 0.86 (0.17), residues: 1032 sheet: 0.71 (0.25), residues: 468 loop : -1.21 (0.19), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 2.301 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 193 average time/residue: 0.3619 time to fit residues: 105.2952 Evaluate side-chains 184 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1794 time to fit residues: 4.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 21048 Z= 0.484 Angle : 0.610 6.854 28686 Z= 0.317 Chirality : 0.047 0.153 3204 Planarity : 0.005 0.053 3702 Dihedral : 4.293 28.892 2874 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2538 helix: 0.75 (0.17), residues: 990 sheet: 0.28 (0.24), residues: 480 loop : -1.44 (0.18), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 2.348 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 186 average time/residue: 0.4057 time to fit residues: 113.3895 Evaluate side-chains 180 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1881 time to fit residues: 5.3158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.8580 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21048 Z= 0.220 Angle : 0.485 6.147 28686 Z= 0.255 Chirality : 0.042 0.137 3204 Planarity : 0.004 0.046 3702 Dihedral : 3.969 29.521 2874 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2538 helix: 0.70 (0.17), residues: 1038 sheet: 0.56 (0.24), residues: 468 loop : -1.30 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 2.353 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 195 average time/residue: 0.3651 time to fit residues: 106.1691 Evaluate side-chains 188 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.502 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1760 time to fit residues: 5.9827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 182 optimal weight: 0.0060 chunk 141 optimal weight: 0.2980 chunk 210 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 21048 Z= 0.130 Angle : 0.438 6.063 28686 Z= 0.229 Chirality : 0.040 0.133 3204 Planarity : 0.003 0.042 3702 Dihedral : 3.609 28.767 2874 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2538 helix: 0.82 (0.17), residues: 1074 sheet: 0.76 (0.25), residues: 468 loop : -1.08 (0.19), residues: 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 2.330 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 198 average time/residue: 0.3743 time to fit residues: 111.0448 Evaluate side-chains 185 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1800 time to fit residues: 5.0128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 158 optimal weight: 0.0870 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21048 Z= 0.126 Angle : 0.442 7.136 28686 Z= 0.227 Chirality : 0.040 0.136 3204 Planarity : 0.004 0.058 3702 Dihedral : 3.450 27.119 2874 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2538 helix: 0.96 (0.17), residues: 1080 sheet: 0.77 (0.24), residues: 480 loop : -1.04 (0.19), residues: 978 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 2.441 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.3683 time to fit residues: 103.7242 Evaluate side-chains 186 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1807 time to fit residues: 3.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8530 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.155 Angle : 0.455 7.705 28686 Z= 0.233 Chirality : 0.041 0.135 3204 Planarity : 0.004 0.062 3702 Dihedral : 3.460 25.877 2874 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2538 helix: 0.98 (0.17), residues: 1080 sheet: 0.90 (0.25), residues: 468 loop : -1.07 (0.19), residues: 990 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.609 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3923 time to fit residues: 102.6944 Evaluate side-chains 173 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.7980 chunk 149 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 204 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 21048 Z= 0.151 Angle : 0.455 7.225 28686 Z= 0.233 Chirality : 0.041 0.135 3204 Planarity : 0.004 0.060 3702 Dihedral : 3.432 24.997 2874 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2538 helix: 1.02 (0.17), residues: 1080 sheet: 1.05 (0.25), residues: 462 loop : -1.02 (0.19), residues: 996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3938 time to fit residues: 103.9285 Evaluate side-chains 175 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108483 restraints weight = 24192.805| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.71 r_work: 0.3030 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21048 Z= 0.206 Angle : 0.482 6.640 28686 Z= 0.248 Chirality : 0.042 0.136 3204 Planarity : 0.004 0.059 3702 Dihedral : 3.581 25.324 2874 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2538 helix: 0.94 (0.17), residues: 1074 sheet: 0.97 (0.25), residues: 462 loop : -0.95 (0.19), residues: 1002 =============================================================================== Job complete usr+sys time: 3589.45 seconds wall clock time: 66 minutes 20.23 seconds (3980.23 seconds total)