Starting phenix.real_space_refine on Sat Nov 18 02:49:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x13_32933/11_2023/7x13_32933.pdb" } resolution = 3.7 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= 0.005 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 105 5.16 5 C 13495 2.51 5 N 3568 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "I GLU 258": "OE1" <-> "OE2" Residue "I GLU 272": "OE1" <-> "OE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 356": "OE1" <-> "OE2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I GLU 388": "OE1" <-> "OE2" Residue "I GLU 430": "OE1" <-> "OE2" Residue "J ARG 344": "NH1" <-> "NH2" Residue "J GLU 345": "OE1" <-> "OE2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "K GLU 272": "OE1" <-> "OE2" Residue "K GLU 356": "OE1" <-> "OE2" Residue "K GLU 388": "OE1" <-> "OE2" Residue "L GLU 269": "OE1" <-> "OE2" Residue "L GLU 283": "OE1" <-> "OE2" Residue "L GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21248 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1783 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "C" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "D" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "F" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "G" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "H" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "I" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "J" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "K" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Time building chain proxies: 10.94, per 1000 atoms: 0.51 Number of scatterers: 21248 At special positions: 0 Unit cell: (186.15, 175.95, 135.15, 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 105 16.00 O 4080 8.00 N 3568 7.00 C 13495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 321 " distance=2.04 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 321 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 425 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 321 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 425 " distance=2.03 Simple disulfide: pdb=" SG CYS G 261 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 261 " - pdb=" SG CYS H 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS I 261 " - pdb=" SG CYS I 321 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 425 " distance=2.03 Simple disulfide: pdb=" SG CYS J 261 " - pdb=" SG CYS J 321 " distance=2.04 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 425 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 321 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 425 " distance=2.03 Simple disulfide: pdb=" SG CYS L 261 " - pdb=" SG CYS L 321 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 425 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 3.8 seconds 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5096 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 67 sheets defined 13.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.803A pdb=" N MET A 358 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.714A pdb=" N TYR A 436 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.137A pdb=" N MET B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.613A pdb=" N TRP C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.576A pdb=" N MET C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 360' Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.890A pdb=" N GLN C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 419' Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.604A pdb=" N TYR C 436 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.686A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 315 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.698A pdb=" N GLN D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 Processing helix chain 'E' and resid 246 through 252 removed outlier: 4.136A pdb=" N MET E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 removed outlier: 3.732A pdb=" N TRP E 313 " --> pdb=" O CYS E 309 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.562A pdb=" N TYR E 436 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 447 removed outlier: 4.395A pdb=" N GLY E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 442 through 447' Processing helix chain 'F' and resid 246 through 252 Processing helix chain 'F' and resid 310 through 316 removed outlier: 3.642A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.722A pdb=" N THR F 359 " --> pdb=" O ARG F 355 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.697A pdb=" N GLN F 419 " --> pdb=" O SER F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 436 removed outlier: 3.510A pdb=" N TYR F 436 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.617A pdb=" N GLY F 446 " --> pdb=" O LYS F 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.869A pdb=" N TRP G 313 " --> pdb=" O CYS G 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 360 removed outlier: 3.611A pdb=" N THR G 359 " --> pdb=" O ARG G 355 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G 360 " --> pdb=" O GLU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 432 through 436 Processing helix chain 'H' and resid 246 through 252 removed outlier: 3.565A pdb=" N MET H 252 " --> pdb=" O LYS H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 316 removed outlier: 3.550A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 Processing helix chain 'H' and resid 414 through 420 removed outlier: 4.068A pdb=" N GLY H 420 " --> pdb=" O ARG H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 436 Processing helix chain 'I' and resid 246 through 252 Processing helix chain 'I' and resid 309 through 316 removed outlier: 4.255A pdb=" N GLY I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 359 Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 432 through 436 removed outlier: 3.559A pdb=" N TYR I 436 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 251 removed outlier: 3.769A pdb=" N THR J 250 " --> pdb=" O LYS J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 316 Processing helix chain 'J' and resid 355 through 360 removed outlier: 3.935A pdb=" N MET J 358 " --> pdb=" O ARG J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 420 removed outlier: 4.214A pdb=" N GLN J 419 " --> pdb=" O SER J 415 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY J 420 " --> pdb=" O ARG J 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 415 through 420' Processing helix chain 'J' and resid 432 through 436 Processing helix chain 'K' and resid 246 through 252 removed outlier: 3.875A pdb=" N THR K 250 " --> pdb=" O LYS K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 316 removed outlier: 3.689A pdb=" N GLY K 316 " --> pdb=" O ASP K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 359 Processing helix chain 'K' and resid 414 through 420 removed outlier: 3.672A pdb=" N GLY K 420 " --> pdb=" O ARG K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 436 removed outlier: 3.562A pdb=" N HIS K 435 " --> pdb=" O LEU K 432 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR K 436 " --> pdb=" O HIS K 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 432 through 436' Processing helix chain 'L' and resid 246 through 251 Processing helix chain 'L' and resid 309 through 316 Processing helix chain 'L' and resid 413 through 420 removed outlier: 3.745A pdb=" N GLY L 420 " --> pdb=" O ARG L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 434 No H-bonds generated for 'chain 'L' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.965A pdb=" N VAL A 262 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.965A pdb=" N VAL A 262 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.668A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 351 removed outlier: 3.793A pdb=" N THR A 366 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 3.793A pdb=" N THR A 366 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 removed outlier: 4.249A pdb=" N PHE A 423 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.854A pdb=" N PHE B 243 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR B 260 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 261 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 304 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'B' and resid 293 through 294 removed outlier: 3.737A pdb=" N GLU B 293 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 301 " --> pdb=" O GLU B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 347 through 351 removed outlier: 3.742A pdb=" N THR B 366 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 383 Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.545A pdb=" N THR C 260 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 274 through 278 Processing sheet with id=AB5, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB6, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.818A pdb=" N THR C 366 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.818A pdb=" N THR C 366 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 377 through 382 removed outlier: 3.739A pdb=" N SER C 424 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 423 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.608A pdb=" N SER D 239 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 260 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 263 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 302 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.608A pdb=" N SER D 239 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 260 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 282 through 283 Processing sheet with id=AC3, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.635A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.635A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 405 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 397 " --> pdb=" O PHE D 405 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 386 through 388 removed outlier: 4.715A pdb=" N TRP D 381 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 449 through 450 removed outlier: 7.461A pdb=" N THR D 449 " --> pdb=" O TYR E 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 258 through 266 removed outlier: 6.532A pdb=" N TYR E 300 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 305 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 288 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 258 through 266 removed outlier: 6.532A pdb=" N TYR E 300 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG E 301 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 293 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 274 through 279 Processing sheet with id=AD1, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.807A pdb=" N THR E 366 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AD3, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AD4, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.660A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 265 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F 305 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS F 288 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.660A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 265 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG F 301 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU F 293 " --> pdb=" O ARG F 301 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AD7, first strand: chain 'F' and resid 347 through 351 removed outlier: 3.575A pdb=" N THR F 366 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE F 404 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AD9, first strand: chain 'G' and resid 239 through 243 removed outlier: 3.704A pdb=" N THR G 260 " --> pdb=" O PHE G 243 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL G 259 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU G 306 " --> pdb=" O VAL G 259 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS G 261 " --> pdb=" O SER G 304 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER G 304 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AE2, first strand: chain 'G' and resid 293 through 294 Processing sheet with id=AE3, first strand: chain 'G' and resid 347 through 351 Processing sheet with id=AE4, first strand: chain 'G' and resid 347 through 351 removed outlier: 3.537A pdb=" N PHE G 405 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AE6, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.629A pdb=" N THR H 260 " --> pdb=" O PHE H 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP H 265 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 300 " --> pdb=" O ASP H 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.629A pdb=" N THR H 260 " --> pdb=" O PHE H 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP H 265 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 300 " --> pdb=" O ASP H 265 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG H 301 " --> pdb=" O GLU H 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU H 293 " --> pdb=" O ARG H 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 274 through 279 removed outlier: 3.547A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.631A pdb=" N THR H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.631A pdb=" N THR H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AF3, first strand: chain 'H' and resid 453 through 454 Processing sheet with id=AF4, first strand: chain 'I' and resid 239 through 243 removed outlier: 4.681A pdb=" N ASP I 265 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR I 300 " --> pdb=" O ASP I 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL I 305 " --> pdb=" O LYS I 288 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 239 through 243 removed outlier: 4.681A pdb=" N ASP I 265 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR I 300 " --> pdb=" O ASP I 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG I 301 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU I 293 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 282 through 284 removed outlier: 4.209A pdb=" N TRP I 277 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 274 " --> pdb=" O SER I 324 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 347 through 351 removed outlier: 3.955A pdb=" N THR I 366 " --> pdb=" O LEU I 351 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY I 371 " --> pdb=" O PHE I 404 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE I 404 " --> pdb=" O GLY I 371 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 378 through 382 removed outlier: 3.637A pdb=" N PHE I 423 " --> pdb=" O LEU I 441 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 239 through 243 removed outlier: 3.576A pdb=" N PHE J 243 " --> pdb=" O THR J 260 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR J 260 " --> pdb=" O PHE J 243 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 282 through 283 Processing sheet with id=AG2, first strand: chain 'J' and resid 347 through 350 removed outlier: 5.290A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 347 through 350 removed outlier: 5.290A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE J 405 " --> pdb=" O VAL J 397 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 386 through 387 removed outlier: 3.984A pdb=" N ALA J 378 " --> pdb=" O MET J 428 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE J 423 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS J 425 " --> pdb=" O LYS J 439 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS J 439 " --> pdb=" O CYS J 425 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 239 through 243 removed outlier: 3.635A pdb=" N VAL K 262 " --> pdb=" O PHE K 241 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE K 243 " --> pdb=" O THR K 260 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 260 " --> pdb=" O PHE K 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 274 through 279 Processing sheet with id=AG7, first strand: chain 'K' and resid 347 through 350 removed outlier: 3.632A pdb=" N GLY K 371 " --> pdb=" O PHE K 404 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE K 404 " --> pdb=" O GLY K 371 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 386 through 387 Processing sheet with id=AG9, first strand: chain 'L' and resid 239 through 243 removed outlier: 4.006A pdb=" N THR L 260 " --> pdb=" O PHE L 243 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 300 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 239 through 243 removed outlier: 4.006A pdb=" N THR L 260 " --> pdb=" O PHE L 243 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 300 " --> pdb=" O ASP L 265 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG L 301 " --> pdb=" O GLU L 293 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 293 " --> pdb=" O ARG L 301 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 282 through 283 removed outlier: 4.681A pdb=" N TYR L 319 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE L 336 " --> pdb=" O TYR L 319 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS L 321 " --> pdb=" O LYS L 334 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS L 334 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 347 through 351 removed outlier: 3.914A pdb=" N THR L 366 " --> pdb=" O LEU L 351 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE L 404 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 386 through 387 removed outlier: 3.575A pdb=" N SER L 383 " --> pdb=" O GLN L 386 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2046 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: 6.88 Time building geometry restraints manager: 8.13 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: 6789 1.34 - 1.46: 4950 1.46 - 1.58: 9935 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 21824 Sorted by residual: bond pdb=" CB PRO A 352 " pdb=" CG PRO A 352 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.04e+00 bond pdb=" CA PHE E 241 " pdb=" CB PHE E 241 " ideal model delta sigma weight residual 1.528 1.564 -0.035 2.61e-02 1.47e+03 1.82e+00 bond pdb=" CG ARG F 255 " pdb=" CD ARG F 255 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C ARG E 255 " pdb=" N THR E 256 " ideal model delta sigma weight residual 1.327 1.350 -0.023 2.31e-02 1.87e+03 1.02e+00 bond pdb=" CG PRO A 352 " pdb=" CD PRO A 352 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.34e-01 ... (remaining 21819 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 953 106.21 - 113.18: 11977 113.18 - 120.15: 6918 120.15 - 127.13: 9485 127.13 - 134.10: 372 Bond angle restraints: 29705 Sorted by residual: angle pdb=" CA PRO A 352 " pdb=" N PRO A 352 " pdb=" CD PRO A 352 " ideal model delta sigma weight residual 112.00 107.62 4.38 1.40e+00 5.10e-01 9.77e+00 angle pdb=" C HIS H 433 " pdb=" N ASN H 434 " pdb=" CA ASN H 434 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 angle pdb=" CA LYS J 246 " pdb=" CB LYS J 246 " pdb=" CG LYS J 246 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" C LYS J 246 " pdb=" CA LYS J 246 " pdb=" CB LYS J 246 " ideal model delta sigma weight residual 109.82 114.31 -4.49 1.65e+00 3.67e-01 7.41e+00 angle pdb=" C SER F 383 " pdb=" N ASN F 384 " pdb=" CA ASN F 384 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 ... (remaining 29700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11973 17.98 - 35.96: 1125 35.96 - 53.94: 190 53.94 - 71.92: 43 71.92 - 89.90: 24 Dihedral angle restraints: 13355 sinusoidal: 5483 harmonic: 7872 Sorted by residual: dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual 93.00 154.66 -61.66 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS C 367 " pdb=" SG CYS C 367 " pdb=" SG CYS C 425 " pdb=" CB CYS C 425 " ideal model delta sinusoidal sigma weight residual 93.00 144.49 -51.49 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CA LYS J 246 " pdb=" C LYS J 246 " pdb=" N PRO J 247 " pdb=" CA PRO J 247 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 13352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2310 0.035 - 0.071: 570 0.071 - 0.106: 281 0.106 - 0.142: 102 0.142 - 0.177: 5 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CB ILE G 336 " pdb=" CA ILE G 336 " pdb=" CG1 ILE G 336 " pdb=" CG2 ILE G 336 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE D 377 " pdb=" N ILE D 377 " pdb=" C ILE D 377 " pdb=" CB ILE D 377 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 3265 not shown) Planarity restraints: 3821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 351 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 352 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 244 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO I 245 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 245 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 245 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 256 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO H 257 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 257 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 257 " -0.029 5.00e-02 4.00e+02 ... (remaining 3818 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 368 2.70 - 3.25: 19384 3.25 - 3.80: 31514 3.80 - 4.35: 39765 4.35 - 4.90: 67473 Nonbonded interactions: 158504 Sorted by model distance: nonbonded pdb=" O GLU K 382 " pdb=" OG SER K 424 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR E 436 " pdb=" NE2 GLN E 438 " model vdw 2.157 2.520 nonbonded pdb=" OG1 THR G 256 " pdb=" O VAL G 308 " model vdw 2.227 2.440 nonbonded pdb=" OD2 ASP G 442 " pdb=" OG SER G 444 " model vdw 2.236 2.440 nonbonded pdb=" NH1 ARG E 255 " pdb=" CG2 THR E 256 " model vdw 2.255 3.540 ... (remaining 158499 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' and resid 236 through 456) selection = (chain 'B' and resid 236 through 456) selection = (chain 'C' and resid 236 through 456) selection = (chain 'D' and resid 236 through 456) selection = (chain 'E' and resid 236 through 456) selection = (chain 'F' and resid 236 through 456) selection = chain 'G' selection = (chain 'H' and resid 236 through 456) selection = (chain 'I' and resid 236 through 456) selection = (chain 'J' and resid 236 through 456) selection = chain 'K' selection = chain 'L' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 54.280 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 21824 Z= 0.130 Angle : 0.507 7.200 29705 Z= 0.264 Chirality : 0.042 0.177 3268 Planarity : 0.003 0.083 3821 Dihedral : 14.422 89.902 8187 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.04 % Allowed : 0.12 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2644 helix: 0.57 (0.39), residues: 195 sheet: 2.23 (0.16), residues: 942 loop : 1.51 (0.16), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.450 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.3148 time to fit residues: 135.1255 Evaluate side-chains 206 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 30.0000 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 0.0670 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 239 optimal weight: 10.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS A 434 ASN B 429 HIS C 362 GLN C 435 HIS E 433 HIS E 438 GLN F 310 HIS ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 419 GLN G 315 ASN ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN J 276 ASN J 361 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS L 315 ASN L 438 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21824 Z= 0.293 Angle : 0.644 8.448 29705 Z= 0.331 Chirality : 0.047 0.167 3268 Planarity : 0.004 0.065 3821 Dihedral : 4.077 19.640 2848 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 1.82 % Allowed : 8.12 % Favored : 90.06 % 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: 2.04 (0.16), residues: 2644 helix: 0.47 (0.37), residues: 210 sheet: 1.98 (0.15), residues: 966 loop : 1.21 (0.16), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 2.542 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 33 residues processed: 245 average time/residue: 0.3076 time to fit residues: 120.9036 Evaluate side-chains 221 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1884 time to fit residues: 15.2223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 213 optimal weight: 40.0000 chunk 238 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 GLN ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 ASN G 433 HIS H 310 HIS ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 310 HIS I 325 ASN I 361 ASN J 315 ASN J 386 GLN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21824 Z= 0.363 Angle : 0.694 9.593 29705 Z= 0.359 Chirality : 0.048 0.178 3268 Planarity : 0.005 0.054 3821 Dihedral : 4.729 22.348 2848 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.46 % Allowed : 12.92 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2644 helix: -0.59 (0.33), residues: 222 sheet: 1.50 (0.15), residues: 974 loop : 0.83 (0.16), residues: 1448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 225 time to evaluate : 2.717 Fit side-chains outliers start: 61 outliers final: 35 residues processed: 271 average time/residue: 0.3061 time to fit residues: 132.7266 Evaluate side-chains 233 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1879 time to fit residues: 16.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 228 optimal weight: 40.0000 chunk 68 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 310 HIS ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN I 421 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21824 Z= 0.403 Angle : 0.723 8.565 29705 Z= 0.375 Chirality : 0.049 0.180 3268 Planarity : 0.005 0.064 3821 Dihedral : 5.198 23.261 2848 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 3.51 % Allowed : 15.47 % Favored : 81.02 % 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: 0.80 (0.15), residues: 2644 helix: -0.93 (0.33), residues: 224 sheet: 1.16 (0.15), residues: 957 loop : 0.46 (0.16), residues: 1463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 206 time to evaluate : 2.423 Fit side-chains revert: symmetry clash outliers start: 87 outliers final: 53 residues processed: 278 average time/residue: 0.3142 time to fit residues: 139.3980 Evaluate side-chains 240 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 2.418 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.1945 time to fit residues: 23.0617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 0.0040 chunk 64 optimal weight: 3.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 434 ASN G 452 ASN H 310 HIS ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 ASN ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21824 Z= 0.192 Angle : 0.588 11.350 29705 Z= 0.298 Chirality : 0.045 0.221 3268 Planarity : 0.004 0.048 3821 Dihedral : 4.562 20.617 2848 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.37 % Allowed : 17.61 % Favored : 81.02 % 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: 1.13 (0.16), residues: 2644 helix: -0.53 (0.35), residues: 215 sheet: 1.38 (0.15), residues: 967 loop : 0.64 (0.16), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 2.228 Fit side-chains outliers start: 34 outliers final: 19 residues processed: 242 average time/residue: 0.3137 time to fit residues: 120.7290 Evaluate side-chains 219 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1907 time to fit residues: 10.2563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21824 Z= 0.151 Angle : 0.543 9.205 29705 Z= 0.273 Chirality : 0.044 0.162 3268 Planarity : 0.004 0.045 3821 Dihedral : 4.156 24.079 2848 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.89 % Allowed : 19.06 % Favored : 80.05 % 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: 1.39 (0.16), residues: 2644 helix: -0.19 (0.36), residues: 215 sheet: 1.54 (0.16), residues: 962 loop : 0.81 (0.16), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 2.632 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 230 average time/residue: 0.3382 time to fit residues: 124.3723 Evaluate side-chains 215 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1996 time to fit residues: 8.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN H 310 HIS ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21824 Z= 0.219 Angle : 0.583 8.989 29705 Z= 0.295 Chirality : 0.045 0.173 3268 Planarity : 0.004 0.046 3821 Dihedral : 4.325 19.643 2848 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.13 % Allowed : 19.31 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2644 helix: -0.25 (0.36), residues: 216 sheet: 1.40 (0.15), residues: 975 loop : 0.80 (0.16), residues: 1453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.404 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 222 average time/residue: 0.3169 time to fit residues: 111.6371 Evaluate side-chains 213 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1940 time to fit residues: 11.0667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 231 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21824 Z= 0.181 Angle : 0.559 8.397 29705 Z= 0.283 Chirality : 0.044 0.173 3268 Planarity : 0.004 0.043 3821 Dihedral : 4.212 18.610 2848 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.73 % Allowed : 19.71 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.16), residues: 2644 helix: -0.14 (0.37), residues: 216 sheet: 1.44 (0.16), residues: 984 loop : 0.83 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 2.526 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 219 average time/residue: 0.3384 time to fit residues: 116.7238 Evaluate side-chains 207 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 2.432 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1910 time to fit residues: 7.4451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 0.0370 chunk 224 optimal weight: 8.9990 chunk 236 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 ASN H 310 HIS ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21824 Z= 0.145 Angle : 0.543 8.511 29705 Z= 0.272 Chirality : 0.043 0.209 3268 Planarity : 0.004 0.044 3821 Dihedral : 4.051 20.572 2848 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.44 % Allowed : 20.19 % Favored : 79.36 % 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 (0.16), residues: 2644 helix: 0.01 (0.38), residues: 216 sheet: 1.56 (0.16), residues: 968 loop : 0.91 (0.16), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 2.443 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 213 average time/residue: 0.3355 time to fit residues: 112.0429 Evaluate side-chains 206 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1928 time to fit residues: 6.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS L 315 ASN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21824 Z= 0.233 Angle : 0.594 8.604 29705 Z= 0.301 Chirality : 0.045 0.167 3268 Planarity : 0.004 0.048 3821 Dihedral : 4.376 19.884 2848 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 0.20 % Allowed : 20.52 % Favored : 79.28 % 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: 1.32 (0.16), residues: 2644 helix: -0.15 (0.37), residues: 210 sheet: 1.41 (0.15), residues: 986 loop : 0.79 (0.16), residues: 1448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 2.439 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 209 average time/residue: 0.3326 time to fit residues: 109.4472 Evaluate side-chains 201 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2016 time to fit residues: 4.9139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN H 310 HIS ** H 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.207962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.189371 restraints weight = 39344.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.186787 restraints weight = 64564.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.185428 restraints weight = 59298.317| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21824 Z= 0.195 Angle : 0.569 9.111 29705 Z= 0.288 Chirality : 0.044 0.208 3268 Planarity : 0.004 0.043 3821 Dihedral : 4.297 19.717 2848 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.57 % Allowed : 20.64 % Favored : 78.80 % 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: 1.37 (0.16), residues: 2644 helix: -0.02 (0.37), residues: 215 sheet: 1.45 (0.15), residues: 995 loop : 0.80 (0.16), residues: 1434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3725.91 seconds wall clock time: 69 minutes 49.40 seconds (4189.40 seconds total)