Starting phenix.real_space_refine on Sat Jul 27 13:50:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/07_2024/8j1h_35922_trim.cif" } resolution = 3.88 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= 0.015 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: 6 Type Number sf(0) Gaussians S 96 5.16 5 C 12480 2.51 5 N 3168 2.21 5 O 3388 1.98 5 F 8 1.80 5 H 19324 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 457": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 38464 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "D" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "B" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "A" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.09, per 1000 atoms: 0.42 Number of scatterers: 38464 At special positions: 0 Unit cell: (160.89, 160.89, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 F 8 9.00 O 3388 8.00 N 3168 7.00 C 12480 6.00 H 19324 1.00 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: 29.33 Conformation dependent library (CDL) restraints added in 3.5 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 65.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.509A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.885A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.582A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.648A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.058A pdb=" N MET C 449 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 450' Processing helix chain 'C' and resid 453 through 467 removed outlier: 3.672A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 490 Processing helix chain 'C' and resid 504 through 531 Processing helix chain 'C' and resid 550 through 570 removed outlier: 3.711A pdb=" N ALA C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 593 removed outlier: 3.763A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 Processing helix chain 'C' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 677 Processing helix chain 'C' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.699A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.509A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 4.199A pdb=" N GLY D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.583A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.647A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 357 removed outlier: 3.800A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 removed outlier: 5.500A pdb=" N HIS D 401 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET D 449 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 445 through 450' Processing helix chain 'D' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 490 Processing helix chain 'D' and resid 504 through 531 Processing helix chain 'D' and resid 550 through 570 removed outlier: 3.711A pdb=" N ALA D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 593 removed outlier: 3.764A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 610 Processing helix chain 'D' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 677 Processing helix chain 'D' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 748 removed outlier: 3.698A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.508A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.581A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.648A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 450' Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 490 Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 550 through 570 removed outlier: 3.712A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 593 removed outlier: 3.764A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 696 through 724 removed outlier: 3.817A pdb=" N THR B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.699A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.508A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.582A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.649A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.688A pdb=" N HIS A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 504 through 531 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.712A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.763A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 748 removed outlier: 3.698A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 410 removed outlier: 3.943A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2928 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: 13.44 Time building geometry restraints manager: 30.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19292 1.03 - 1.23: 54 1.23 - 1.42: 8234 1.42 - 1.62: 11160 1.62 - 1.82: 160 Bond restraints: 38900 Sorted by residual: bond pdb=" C7 9QM D 901 " pdb=" O1 9QM D 901 " ideal model delta sigma weight residual 1.213 1.398 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C7 9QM B 901 " pdb=" O1 9QM B 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C7 9QM A 901 " pdb=" O1 9QM A 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C7 9QM C 901 " pdb=" O1 9QM C 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C23 9QM B 901 " pdb=" C25 9QM B 901 " ideal model delta sigma weight residual 1.382 1.526 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 38895 not shown) Histogram of bond angle deviations from ideal: 71.51 - 84.05: 36 84.05 - 96.58: 0 96.58 - 109.12: 22377 109.12 - 121.66: 41346 121.66 - 134.19: 6457 Bond angle restraints: 70216 Sorted by residual: angle pdb=" C SER D 688 " pdb=" CA SER D 688 " pdb=" HA SER D 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER C 688 " pdb=" CA SER C 688 " pdb=" HA SER C 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER A 688 " pdb=" CA SER A 688 " pdb=" HA SER A 688 " ideal model delta sigma weight residual 109.00 71.53 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER B 688 " pdb=" CA SER B 688 " pdb=" HA SER B 688 " ideal model delta sigma weight residual 109.00 71.55 37.45 3.00e+00 1.11e-01 1.56e+02 angle pdb=" N ILE C 696 " pdb=" CA ILE C 696 " pdb=" HA ILE C 696 " ideal model delta sigma weight residual 110.00 73.76 36.24 3.00e+00 1.11e-01 1.46e+02 ... (remaining 70211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16306 17.76 - 35.53: 1445 35.53 - 53.29: 377 53.29 - 71.06: 84 71.06 - 88.82: 16 Dihedral angle restraints: 18228 sinusoidal: 9836 harmonic: 8392 Sorted by residual: dihedral pdb=" CA LYS C 727 " pdb=" C LYS C 727 " pdb=" N GLU C 728 " pdb=" CA GLU C 728 " ideal model delta harmonic sigma weight residual 180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS B 727 " pdb=" C LYS B 727 " pdb=" N GLU B 728 " pdb=" CA GLU B 728 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS A 727 " pdb=" C LYS A 727 " pdb=" N GLU A 728 " pdb=" CA GLU A 728 " ideal model delta harmonic sigma weight residual 180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 3020 0.276 - 0.552: 8 0.552 - 0.829: 0 0.829 - 1.105: 0 1.105 - 1.381: 4 Chirality restraints: 3032 Sorted by residual: chirality pdb=" CB THR B 701 " pdb=" CA THR B 701 " pdb=" OG1 THR B 701 " pdb=" CG2 THR B 701 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.77e+01 chirality pdb=" CB THR A 701 " pdb=" CA THR A 701 " pdb=" OG1 THR A 701 " pdb=" CG2 THR A 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CB THR C 701 " pdb=" CA THR C 701 " pdb=" OG1 THR C 701 " pdb=" CG2 THR C 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.73e+01 ... (remaining 3029 not shown) Planarity restraints: 5540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 737 " 0.024 2.00e-02 2.50e+03 1.40e-02 7.86e+00 pdb=" CG TRP C 737 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 737 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 737 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 737 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 737 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 737 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 737 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP C 737 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP C 737 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 737 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 737 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP C 737 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 737 " -0.024 2.00e-02 2.50e+03 1.40e-02 7.82e+00 pdb=" CG TRP A 737 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 737 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 737 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 737 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 737 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 737 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 737 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 737 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 737 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 737 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 737 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 737 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 737 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 737 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 737 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 737 " -0.024 2.00e-02 2.50e+03 1.40e-02 7.80e+00 pdb=" CG TRP D 737 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP D 737 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 737 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 737 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 737 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 737 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 737 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP D 737 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP D 737 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 737 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 737 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP D 737 " -0.001 2.00e-02 2.50e+03 ... (remaining 5537 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1800 2.14 - 2.76: 76208 2.76 - 3.37: 113496 3.37 - 3.99: 137626 3.99 - 4.60: 213897 Nonbonded interactions: 543027 Sorted by model distance: nonbonded pdb="HD22 ASN D 474 " pdb=" O1 9QM D 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN A 474 " pdb=" O1 9QM A 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN B 474 " pdb=" O1 9QM B 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN C 474 " pdb=" O1 9QM C 901 " model vdw 1.526 1.850 nonbonded pdb=" OD1 ASP B 318 " pdb=" H ASN B 322 " model vdw 1.543 1.850 ... (remaining 543022 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' } 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: 1.560 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: 0.580 Extract box with map and model: 1.360 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 111.620 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 : 0.009 0.185 19576 Z= 0.539 Angle : 0.757 11.030 26524 Z= 0.414 Chirality : 0.067 1.381 3032 Planarity : 0.004 0.036 3280 Dihedral : 13.707 73.260 7148 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.00 % Favored : 87.48 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % 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 (0.18), residues: 2316 helix: 0.33 (0.15), residues: 1264 sheet: -0.17 (0.67), residues: 64 loop : -2.57 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 737 HIS 0.003 0.001 HIS C 388 PHE 0.036 0.002 PHE B 524 TYR 0.034 0.002 TYR C 346 ARG 0.004 0.001 ARG D 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 318 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 271 ARG cc_start: 0.7609 (tpm170) cc_final: 0.7167 (tpp-160) REVERT: D 271 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7113 (tpp-160) REVERT: B 271 ARG cc_start: 0.7727 (tpm170) cc_final: 0.7287 (tpp-160) REVERT: A 271 ARG cc_start: 0.7641 (tpm170) cc_final: 0.7166 (tpp-160) REVERT: A 578 MET cc_start: 0.7695 (tmm) cc_final: 0.7425 (tmm) REVERT: A 742 LEU cc_start: 0.8528 (mm) cc_final: 0.8157 (tp) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.6651 time to fit residues: 323.4615 Evaluate side-chains 266 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 181 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19576 Z= 0.241 Angle : 0.685 11.486 26524 Z= 0.369 Chirality : 0.068 1.472 3032 Planarity : 0.005 0.060 3280 Dihedral : 5.404 59.862 2669 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.27 % Favored : 88.21 % Rotamer: Outliers : 1.15 % Allowed : 6.91 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2316 helix: 0.11 (0.14), residues: 1304 sheet: -0.19 (0.67), residues: 64 loop : -2.61 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 737 HIS 0.003 0.001 HIS A 309 PHE 0.023 0.002 PHE B 524 TYR 0.021 0.002 TYR B 346 ARG 0.005 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 482 MET cc_start: 0.6753 (mmp) cc_final: 0.6334 (mmt) REVERT: A 578 MET cc_start: 0.7663 (tmm) cc_final: 0.7446 (tmm) outliers start: 24 outliers final: 21 residues processed: 287 average time/residue: 0.6787 time to fit residues: 294.1767 Evaluate side-chains 299 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 278 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 175 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 0.0770 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19576 Z= 0.387 Angle : 0.730 11.141 26524 Z= 0.397 Chirality : 0.068 1.443 3032 Planarity : 0.005 0.067 3280 Dihedral : 5.683 59.041 2669 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 12.87 % Favored : 86.53 % Rotamer: Outliers : 1.34 % Allowed : 9.98 % Favored : 88.68 % 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: -1.83 (0.17), residues: 2316 helix: -0.16 (0.14), residues: 1300 sheet: -0.55 (0.66), residues: 64 loop : -2.81 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 737 HIS 0.003 0.001 HIS A 401 PHE 0.029 0.002 PHE B 524 TYR 0.028 0.002 TYR B 411 ARG 0.006 0.001 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 346 TYR cc_start: 0.8511 (t80) cc_final: 0.8127 (t80) REVERT: C 482 MET cc_start: 0.6741 (mmp) cc_final: 0.6307 (mmp) REVERT: D 346 TYR cc_start: 0.8455 (t80) cc_final: 0.8105 (t80) REVERT: B 346 TYR cc_start: 0.8497 (t80) cc_final: 0.8156 (t80) REVERT: A 482 MET cc_start: 0.6786 (mmp) cc_final: 0.6576 (mmp) outliers start: 28 outliers final: 23 residues processed: 290 average time/residue: 0.7192 time to fit residues: 317.6986 Evaluate side-chains 293 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 270 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19576 Z= 0.217 Angle : 0.659 11.370 26524 Z= 0.351 Chirality : 0.067 1.447 3032 Planarity : 0.004 0.046 3280 Dihedral : 5.384 59.848 2669 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.05 % Favored : 87.44 % Rotamer: Outliers : 1.10 % Allowed : 12.62 % Favored : 86.28 % 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: -1.44 (0.17), residues: 2316 helix: 0.21 (0.14), residues: 1292 sheet: -0.64 (0.64), residues: 64 loop : -2.68 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 737 HIS 0.002 0.000 HIS A 731 PHE 0.015 0.001 PHE B 524 TYR 0.020 0.002 TYR D 553 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 281 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6830 (mmp) cc_final: 0.6268 (mmp) REVERT: B 346 TYR cc_start: 0.8369 (t80) cc_final: 0.7944 (t80) REVERT: B 482 MET cc_start: 0.6993 (mmp) cc_final: 0.6668 (mmt) REVERT: A 223 MET cc_start: 0.6073 (ppp) cc_final: 0.5825 (ppp) REVERT: A 482 MET cc_start: 0.6779 (mmp) cc_final: 0.6185 (mmp) outliers start: 23 outliers final: 15 residues processed: 287 average time/residue: 0.7716 time to fit residues: 340.3773 Evaluate side-chains 289 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19576 Z= 0.332 Angle : 0.704 11.319 26524 Z= 0.381 Chirality : 0.067 1.443 3032 Planarity : 0.005 0.080 3280 Dihedral : 5.535 59.983 2669 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.30 % Favored : 86.18 % Rotamer: Outliers : 1.78 % Allowed : 12.67 % Favored : 85.56 % 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: -1.60 (0.17), residues: 2316 helix: 0.09 (0.14), residues: 1292 sheet: -0.58 (0.66), residues: 64 loop : -2.79 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 737 HIS 0.002 0.001 HIS B 401 PHE 0.027 0.002 PHE B 524 TYR 0.033 0.002 TYR B 553 ARG 0.010 0.001 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 275 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.7058 (mmp) cc_final: 0.6472 (mmp) REVERT: D 346 TYR cc_start: 0.8444 (t80) cc_final: 0.7995 (t80) REVERT: D 616 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.6979 (ttp-170) REVERT: B 346 TYR cc_start: 0.8482 (t80) cc_final: 0.8021 (t80) REVERT: B 482 MET cc_start: 0.7002 (mmp) cc_final: 0.6635 (mmt) REVERT: A 482 MET cc_start: 0.6925 (mmp) cc_final: 0.6252 (mmp) outliers start: 37 outliers final: 33 residues processed: 293 average time/residue: 0.7084 time to fit residues: 318.3363 Evaluate side-chains 304 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19576 Z= 0.234 Angle : 0.668 11.275 26524 Z= 0.357 Chirality : 0.066 1.422 3032 Planarity : 0.004 0.058 3280 Dihedral : 5.337 58.968 2669 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.44 % Favored : 88.04 % Rotamer: Outliers : 1.68 % Allowed : 13.82 % Favored : 84.50 % 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: -1.36 (0.17), residues: 2316 helix: 0.38 (0.14), residues: 1268 sheet: -0.61 (0.65), residues: 64 loop : -2.74 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 737 HIS 0.002 0.000 HIS A 731 PHE 0.032 0.002 PHE A 524 TYR 0.029 0.002 TYR D 553 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6932 (mmp) cc_final: 0.6391 (mmp) REVERT: D 482 MET cc_start: 0.6998 (mmp) cc_final: 0.6407 (mmp) REVERT: A 482 MET cc_start: 0.6841 (mmp) cc_final: 0.6256 (mmp) outliers start: 35 outliers final: 24 residues processed: 298 average time/residue: 0.7225 time to fit residues: 329.4943 Evaluate side-chains 298 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 274 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 739 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19576 Z= 0.283 Angle : 0.683 11.427 26524 Z= 0.368 Chirality : 0.066 1.446 3032 Planarity : 0.005 0.056 3280 Dihedral : 5.371 59.627 2669 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.82 % Favored : 86.66 % Rotamer: Outliers : 2.06 % Allowed : 14.40 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2316 helix: 0.21 (0.14), residues: 1304 sheet: -0.63 (0.67), residues: 64 loop : -2.72 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.032 0.002 PHE D 524 TYR 0.023 0.002 TYR B 553 ARG 0.005 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.7066 (mmp) cc_final: 0.6510 (mmp) REVERT: D 482 MET cc_start: 0.7046 (mmp) cc_final: 0.6435 (mmp) REVERT: B 482 MET cc_start: 0.6966 (mmp) cc_final: 0.6651 (mmt) REVERT: A 482 MET cc_start: 0.6942 (mmp) cc_final: 0.6355 (mmp) REVERT: A 680 MET cc_start: 0.6280 (mmm) cc_final: 0.6064 (mmm) outliers start: 43 outliers final: 36 residues processed: 308 average time/residue: 0.6722 time to fit residues: 317.3270 Evaluate side-chains 307 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19576 Z= 0.239 Angle : 0.675 11.416 26524 Z= 0.361 Chirality : 0.066 1.446 3032 Planarity : 0.004 0.052 3280 Dihedral : 5.272 59.077 2669 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.00 % Favored : 87.48 % Rotamer: Outliers : 2.11 % Allowed : 14.59 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2316 helix: 0.34 (0.14), residues: 1304 sheet: -0.64 (0.67), residues: 64 loop : -2.66 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.027 0.002 PHE D 524 TYR 0.024 0.002 TYR B 553 ARG 0.008 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 274 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6986 (mmp) cc_final: 0.6438 (mmp) REVERT: D 482 MET cc_start: 0.6934 (mmp) cc_final: 0.6349 (mmp) REVERT: A 482 MET cc_start: 0.6922 (mmp) cc_final: 0.6339 (mmp) outliers start: 44 outliers final: 41 residues processed: 302 average time/residue: 0.6837 time to fit residues: 317.1223 Evaluate side-chains 311 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19576 Z= 0.243 Angle : 0.670 11.455 26524 Z= 0.360 Chirality : 0.066 1.459 3032 Planarity : 0.004 0.051 3280 Dihedral : 5.230 58.895 2669 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.61 % Favored : 86.87 % Rotamer: Outliers : 2.35 % Allowed : 14.59 % Favored : 83.06 % 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: -1.24 (0.17), residues: 2316 helix: 0.40 (0.14), residues: 1304 sheet: -0.66 (0.68), residues: 64 loop : -2.66 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.025 0.002 PHE D 524 TYR 0.024 0.002 TYR B 553 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 275 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6986 (mmp) cc_final: 0.6428 (mmp) REVERT: D 482 MET cc_start: 0.6934 (mmp) cc_final: 0.6347 (mmp) REVERT: A 482 MET cc_start: 0.6920 (mmp) cc_final: 0.6325 (mmp) outliers start: 49 outliers final: 46 residues processed: 308 average time/residue: 0.6762 time to fit residues: 319.8531 Evaluate side-chains 318 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 272 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19576 Z= 0.239 Angle : 0.676 11.461 26524 Z= 0.360 Chirality : 0.067 1.455 3032 Planarity : 0.004 0.050 3280 Dihedral : 5.185 59.345 2669 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.70 % Favored : 87.78 % Rotamer: Outliers : 2.35 % Allowed : 14.78 % Favored : 82.87 % 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: -1.16 (0.17), residues: 2316 helix: 0.47 (0.14), residues: 1304 sheet: -0.69 (0.68), residues: 64 loop : -2.62 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.024 0.002 PHE D 524 TYR 0.024 0.002 TYR B 553 ARG 0.004 0.000 ARG B 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 275 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6990 (mmp) cc_final: 0.6426 (mmp) REVERT: D 482 MET cc_start: 0.6936 (mmp) cc_final: 0.6344 (mmp) REVERT: A 482 MET cc_start: 0.6916 (mmp) cc_final: 0.6324 (mmp) outliers start: 49 outliers final: 44 residues processed: 308 average time/residue: 0.6789 time to fit residues: 320.7385 Evaluate side-chains 317 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.169467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.135244 restraints weight = 143470.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.140920 restraints weight = 74309.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.144480 restraints weight = 49832.236| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19576 Z= 0.175 Angle : 0.654 11.516 26524 Z= 0.345 Chirality : 0.066 1.442 3032 Planarity : 0.004 0.051 3280 Dihedral : 4.981 57.971 2669 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.28 % Favored : 89.38 % Rotamer: Outliers : 1.58 % Allowed : 15.45 % Favored : 82.97 % 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: -0.88 (0.18), residues: 2316 helix: 0.71 (0.14), residues: 1308 sheet: -0.27 (0.69), residues: 64 loop : -2.56 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 737 HIS 0.002 0.001 HIS C 243 PHE 0.020 0.001 PHE A 624 TYR 0.024 0.001 TYR B 553 ARG 0.004 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7302.66 seconds wall clock time: 128 minutes 40.30 seconds (7720.30 seconds total)