Starting phenix.real_space_refine on Wed Nov 20 08:15:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yig_33858/11_2024/7yig_33858.cif" } resolution = 3.6 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= 0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.74, per 1000 atoms: 0.64 Number of scatterers: 21320 At special positions: 0 Unit cell: (157.065, 157.065, 130.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 5.05 Conformation dependent library (CDL) restraints added in 2.9 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 50.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.739A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 247 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.022A pdb=" N LYS A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.515A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 476 removed outlier: 3.720A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.959A pdb=" N ARG A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 Processing helix chain 'A' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG B 160 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 329 through 337 removed outlier: 4.023A pdb=" N LYS B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 358 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 476 removed outlier: 3.721A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.955A pdb=" N ARG B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 520 through 527 Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 546' Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG C 160 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 247 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.023A pdb=" N LYS C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 358 " --> pdb=" O CYS C 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 476 removed outlier: 3.721A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 457 " --> pdb=" O MET C 453 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.954A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 546' Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 692 Processing helix chain 'D' and resid 15 through 22 removed outlier: 3.739A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG D 160 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 161 " --> pdb=" O ASN D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 161' Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP D 217 " --> pdb=" O PHE D 213 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 247 through 265 Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 329 through 337 removed outlier: 4.022A pdb=" N LYS D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE D 356 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 358 " --> pdb=" O CYS D 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS D 361 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 395 Processing helix chain 'D' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 476 removed outlier: 3.720A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 454 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 457 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.953A pdb=" N ARG D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 546' Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AA9, first strand: chain 'B' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AB5, first strand: chain 'C' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 94 through 97 Processing sheet with id=AB9, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AC1, first strand: chain 'D' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2532 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: 7.38 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6704 1.34 - 1.46: 5196 1.46 - 1.58: 9712 1.58 - 1.70: 0 1.70 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CB ARG B 330 " pdb=" CG ARG B 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG D 330 " pdb=" CG ARG D 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG C 330 " pdb=" CG ARG C 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG A 330 " pdb=" CG ARG A 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CA ASP C 601 " pdb=" CB ASP C 601 " ideal model delta sigma weight residual 1.529 1.541 -0.012 1.58e-02 4.01e+03 6.23e-01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 28631 1.39 - 2.77: 800 2.77 - 4.16: 101 4.16 - 5.54: 28 5.54 - 6.93: 24 Bond angle restraints: 29584 Sorted by residual: angle pdb=" C THR C 441 " pdb=" N THR C 442 " pdb=" CA THR C 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR A 441 " pdb=" N THR A 442 " pdb=" CA THR A 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR D 441 " pdb=" N THR D 442 " pdb=" CA THR D 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR B 441 " pdb=" N THR B 442 " pdb=" CA THR B 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N TRP A 292 " pdb=" CA TRP A 292 " pdb=" C TRP A 292 " ideal model delta sigma weight residual 110.44 113.80 -3.36 1.20e+00 6.94e-01 7.86e+00 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11707 17.97 - 35.95: 967 35.95 - 53.92: 206 53.92 - 71.89: 29 71.89 - 89.86: 23 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR B 291 " pdb=" C THR B 291 " pdb=" N TRP B 292 " pdb=" CA TRP B 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR C 291 " pdb=" C THR C 291 " pdb=" N TRP C 292 " pdb=" CA TRP C 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR A 291 " pdb=" C THR A 291 " pdb=" N TRP A 292 " pdb=" CA TRP A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1853 0.029 - 0.058: 1081 0.058 - 0.087: 301 0.087 - 0.116: 137 0.116 - 0.144: 32 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE D 438 " pdb=" N ILE D 438 " pdb=" C ILE D 438 " pdb=" CB ILE D 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 438 " pdb=" N ILE A 438 " pdb=" C ILE A 438 " pdb=" CB ILE A 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 13 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ASN B 13 " 0.025 2.00e-02 2.50e+03 pdb=" O ASN B 13 " -0.009 2.00e-02 2.50e+03 pdb=" N THR B 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 13 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ASN C 13 " 0.025 2.00e-02 2.50e+03 pdb=" O ASN C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N THR C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 13 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C ASN D 13 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN D 13 " 0.009 2.00e-02 2.50e+03 pdb=" N THR D 14 " 0.008 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 2268 2.75 - 3.35: 24023 3.35 - 3.94: 37664 3.94 - 4.54: 51378 4.54 - 5.14: 80844 Nonbonded interactions: 196177 Sorted by model distance: nonbonded pdb=" OH TYR A 195 " pdb=" OE2 GLU B 596 " model vdw 2.152 3.040 nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR D 195 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 195 " pdb=" OE2 GLU C 596 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR C 195 " pdb=" OE2 GLU D 596 " model vdw 2.152 3.040 nonbonded pdb=" O LEU D 418 " pdb=" OG SER D 422 " model vdw 2.257 3.040 ... (remaining 196172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 47.840 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.026 21804 Z= 0.178 Angle : 0.575 6.931 29584 Z= 0.315 Chirality : 0.041 0.144 3404 Planarity : 0.003 0.030 3668 Dihedral : 14.209 89.864 7884 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.80 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -2.00 (0.16), residues: 2616 helix: 0.32 (0.16), residues: 1200 sheet: -3.52 (0.36), residues: 192 loop : -2.74 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 388 HIS 0.003 0.001 HIS C 176 PHE 0.019 0.002 PHE B 293 TYR 0.018 0.001 TYR D 460 ARG 0.002 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2954 time to fit residues: 160.1319 Evaluate side-chains 284 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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: 3.9990 chunk 200 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN A 479 ASN A 579 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 479 ASN B 579 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 479 ASN C 579 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 479 ASN D 579 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21804 Z= 0.166 Angle : 0.530 7.918 29584 Z= 0.280 Chirality : 0.041 0.158 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.384 25.948 2864 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.20 % Rotamer: Outliers : 0.34 % Allowed : 7.23 % Favored : 92.44 % 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: -1.89 (0.16), residues: 2616 helix: 0.37 (0.15), residues: 1288 sheet: -3.40 (0.37), residues: 192 loop : -2.87 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.002 0.001 HIS C 539 PHE 0.010 0.001 PHE C 258 TYR 0.012 0.001 TYR B 460 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 2.324 Fit side-chains REVERT: A 453 MET cc_start: 0.8668 (mtt) cc_final: 0.8291 (mtt) REVERT: A 601 ASP cc_start: 0.7662 (t0) cc_final: 0.7454 (t0) REVERT: B 453 MET cc_start: 0.8709 (mtt) cc_final: 0.8357 (mtt) REVERT: C 453 MET cc_start: 0.8688 (mtt) cc_final: 0.8332 (mtt) REVERT: D 453 MET cc_start: 0.8688 (mtt) cc_final: 0.8328 (mtt) outliers start: 8 outliers final: 4 residues processed: 331 average time/residue: 0.3088 time to fit residues: 163.2316 Evaluate side-chains 290 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 286 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 199 optimal weight: 0.0040 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 213 optimal weight: 0.0370 chunk 238 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1420 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: