Starting phenix.real_space_refine on Thu Sep 18 08:00:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mv0_48650/09_2025/9mv0_48650.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9309 2.51 5 N 2407 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14631 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5686 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 30, 'TRANS': 661} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5686 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 30, 'TRANS': 661} Chain: "D" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.64, per 1000 atoms: 0.25 Number of scatterers: 14631 At special positions: 0 Unit cell: (149, 99, 144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2823 8.00 N 2407 7.00 C 9309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 541 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 415 " distance=2.02 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 486 " distance=2.03 Simple disulfide: pdb=" SG CYS D 445 " - pdb=" SG CYS D 583 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 532 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 545 " " NAG A 902 " - " ASN A 279 " " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 215 " " NAG C 901 " - " ASN C 545 " " NAG C 902 " - " ASN C 279 " " NAG C 903 " - " ASN C 103 " " NAG C 904 " - " ASN C 215 " " NAG E 1 " - " ASN A 386 " " NAG F 1 " - " ASN A 688 " " NAG G 1 " - " ASN C 386 " " NAG H 1 " - " ASN C 688 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 617.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 54.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 53 removed outlier: 3.798A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.703A pdb=" N ALA A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.679A pdb=" N GLN A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 156 through 174 removed outlier: 4.045A pdb=" N GLN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 219 through 248 removed outlier: 4.360A pdb=" N GLU A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.758A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.064A pdb=" N MET A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.690A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.315A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 329' Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.559A pdb=" N ALA A 383 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.999A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.929A pdb=" N THR A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.533A pdb=" N PHE A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 465 " --> pdb=" O MET A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 483 removed outlier: 3.832A pdb=" N GLU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.769A pdb=" N LEU A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.575A pdb=" N ASN A 507 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 508 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.938A pdb=" N THR A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.218A pdb=" N LEU A 559 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 removed outlier: 4.208A pdb=" N THR A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.919A pdb=" N GLU A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.771A pdb=" N ALA A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 removed outlier: 3.725A pdb=" N VAL A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 419 through 426 removed outlier: 4.494A pdb=" N PHE B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.578A pdb=" N THR B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.890A pdb=" N GLN B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 475 removed outlier: 3.951A pdb=" N GLN B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 removed outlier: 3.501A pdb=" N GLY B 539 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 55 through 81 removed outlier: 4.182A pdb=" N LYS C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.575A pdb=" N GLN C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 109 through 129 Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.697A pdb=" N ASP C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 174 removed outlier: 4.098A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 Processing helix chain 'C' and resid 197 through 204 Processing helix chain 'C' and resid 217 through 248 removed outlier: 3.933A pdb=" N LEU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) Proline residue: C 234 - end of helix removed outlier: 3.747A pdb=" N MET C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.476A pdb=" N MET C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.522A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 3.781A pdb=" N ARG C 328 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 384 removed outlier: 4.007A pdb=" N TYR C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 398 through 412 removed outlier: 4.418A pdb=" N GLY C 404 " --> pdb=" O HIS C 400 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.925A pdb=" N THR C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 removed outlier: 4.527A pdb=" N PHE C 451 " --> pdb=" O GLY C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 470 No H-bonds generated for 'chain 'C' and resid 468 through 470' Processing helix chain 'C' and resid 471 through 483 removed outlier: 3.649A pdb=" N LYS C 475 " --> pdb=" O GLN C 471 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP C 476 " --> pdb=" O TRP C 472 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 removed outlier: 3.857A pdb=" N LEU C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 508 removed outlier: 3.667A pdb=" N ASP C 508 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.939A pdb=" N THR C 516 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C 522 " --> pdb=" O THR C 518 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 547 through 559 removed outlier: 4.036A pdb=" N LEU C 559 " --> pdb=" O ASP C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 563 removed outlier: 4.312A pdb=" N THR C 563 " --> pdb=" O GLY C 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 560 through 563' Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.560A pdb=" N ILE C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 587 through 595 Processing helix chain 'C' and resid 621 through 627 removed outlier: 3.917A pdb=" N LEU C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 657 removed outlier: 3.603A pdb=" N LEU C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 705 removed outlier: 3.721A pdb=" N VAL C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 397 Processing helix chain 'D' and resid 418 through 426 removed outlier: 3.663A pdb=" N LEU D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.737A pdb=" N THR D 443 " --> pdb=" O SER D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 465 removed outlier: 3.810A pdb=" N GLN D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 removed outlier: 3.971A pdb=" N GLN D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 removed outlier: 3.522A pdb=" N GLY D 539 " --> pdb=" O ALA D 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.965A pdb=" N VAL A 132 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 5.904A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 418 removed outlier: 6.065A pdb=" N TYR B 417 " --> pdb=" O MET B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 430 through 433 removed outlier: 3.944A pdb=" N GLU B 430 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN B 566 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 456 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 504 through 513 removed outlier: 6.943A pdb=" N THR B 555 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS B 511 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 553 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 261 through 262 removed outlier: 5.830A pdb=" N LEU C 261 " --> pdb=" O VAL C 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 346 through 351 removed outlier: 5.846A pdb=" N ASP C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 430 through 433 removed outlier: 3.833A pdb=" N GLU D 430 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 504 through 513 removed outlier: 5.615A pdb=" N ALA D 506 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR D 559 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU D 508 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR D 557 " --> pdb=" O LEU D 508 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1746 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: 2.18 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4605 1.34 - 1.46: 3799 1.46 - 1.58: 6452 1.58 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 15008 Sorted by residual: bond pdb=" N TYR C 19 " pdb=" CA TYR C 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLN B 389 " pdb=" CA GLN B 389 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N TYR A 19 " pdb=" CA TYR A 19 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N GLN D 389 " pdb=" CA GLN D 389 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" CB TRP C 162 " pdb=" CG TRP C 162 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.17e+00 ... (remaining 15003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 19642 1.31 - 2.63: 539 2.63 - 3.94: 114 3.94 - 5.26: 32 5.26 - 6.57: 6 Bond angle restraints: 20333 Sorted by residual: angle pdb=" C SER B 534 " pdb=" CA SER B 534 " pdb=" CB SER B 534 " ideal model delta sigma weight residual 117.23 110.66 6.57 1.36e+00 5.41e-01 2.34e+01 angle pdb=" N TYR A 206 " pdb=" CA TYR A 206 " pdb=" CB TYR A 206 " ideal model delta sigma weight residual 114.17 109.66 4.51 1.14e+00 7.69e-01 1.57e+01 angle pdb=" C LYS A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 120.72 114.87 5.85 1.67e+00 3.59e-01 1.23e+01 angle pdb=" N PHE A 32 " pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " ideal model delta sigma weight residual 110.39 115.88 -5.49 1.66e+00 3.63e-01 1.09e+01 angle pdb=" CA SER B 534 " pdb=" C SER B 534 " pdb=" N LEU B 535 " ideal model delta sigma weight residual 119.98 117.38 2.60 8.50e-01 1.38e+00 9.36e+00 ... (remaining 20328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8369 17.98 - 35.96: 681 35.96 - 53.93: 140 53.93 - 71.91: 25 71.91 - 89.89: 8 Dihedral angle restraints: 9223 sinusoidal: 3979 harmonic: 5244 Sorted by residual: dihedral pdb=" CA TYR D 446 " pdb=" C TYR D 446 " pdb=" N SER D 447 " pdb=" CA SER D 447 " ideal model delta harmonic sigma weight residual -180.00 -146.62 -33.38 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 45.19 47.81 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CA TYR B 446 " pdb=" C TYR B 446 " pdb=" N SER B 447 " pdb=" CA SER B 447 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 9220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1821 0.044 - 0.088: 273 0.088 - 0.132: 96 0.132 - 0.176: 6 0.176 - 0.220: 2 Chirality restraints: 2198 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 688 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 688 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.11e+00 ... (remaining 2195 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 162 " -0.020 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP C 162 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 162 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 162 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 162 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 162 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 162 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 162 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 162 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 162 " 0.019 2.00e-02 2.50e+03 1.21e-02 3.68e+00 pdb=" CG TRP A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 162 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 162 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 162 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 162 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 661 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 662 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " 0.022 5.00e-02 4.00e+02 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 222 2.60 - 3.18: 14112 3.18 - 3.75: 22185 3.75 - 4.33: 28104 4.33 - 4.90: 45163 Nonbonded interactions: 109786 Sorted by model distance: nonbonded pdb=" OD1 ASP C 226 " pdb=" OH TYR C 453 " model vdw 2.030 3.040 nonbonded pdb=" OG1 THR A 55 " pdb=" OD1 ASN A 58 " model vdw 2.048 3.040 nonbonded pdb=" O PRO D 395 " pdb=" OG1 THR D 398 " model vdw 2.048 3.040 nonbonded pdb=" OG SER D 447 " pdb=" O TYR D 575 " model vdw 2.051 3.040 nonbonded pdb=" OG SER B 447 " pdb=" O TYR B 575 " model vdw 2.080 3.040 ... (remaining 109781 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 389 through 427 or resid 429 through 585)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 0.046 15038 Z= 0.128 Angle : 0.579 6.572 20409 Z= 0.316 Chirality : 0.037 0.220 2198 Planarity : 0.003 0.040 2584 Dihedral : 13.326 89.890 5807 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.21), residues: 1761 helix: 1.10 (0.19), residues: 810 sheet: -0.69 (0.54), residues: 115 loop : -1.54 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 664 TYR 0.020 0.001 TYR A 73 PHE 0.014 0.001 PHE A 32 TRP 0.033 0.001 TRP C 162 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00259 (15008) covalent geometry : angle 0.57082 (20333) SS BOND : bond 0.00303 ( 14) SS BOND : angle 0.83171 ( 28) hydrogen bonds : bond 0.14439 ( 622) hydrogen bonds : angle 5.98360 ( 1746) link_BETA1-4 : bond 0.00637 ( 4) link_BETA1-4 : angle 1.71540 ( 12) link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 2.05426 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9344 (p0) cc_final: 0.9140 (p0) REVERT: A 296 MET cc_start: 0.7386 (ptt) cc_final: 0.6747 (ptp) REVERT: A 350 LEU cc_start: 0.8576 (mt) cc_final: 0.8333 (mt) REVERT: A 382 MET cc_start: 0.7659 (tpt) cc_final: 0.7403 (tpt) REVERT: A 654 LEU cc_start: 0.8800 (mm) cc_final: 0.8550 (tt) REVERT: B 421 LYS cc_start: 0.9301 (pptt) cc_final: 0.8676 (mmtt) REVERT: B 574 GLN cc_start: 0.9207 (tt0) cc_final: 0.8401 (mp10) REVERT: C 67 ASN cc_start: 0.9442 (p0) cc_final: 0.9202 (p0) REVERT: C 222 MET cc_start: 0.8193 (mpp) cc_final: 0.7676 (mpp) REVERT: C 248 MET cc_start: 0.8541 (ppp) cc_final: 0.8239 (ppp) REVERT: C 301 TRP cc_start: 0.7986 (m100) cc_final: 0.7786 (m100) REVERT: C 350 LEU cc_start: 0.8853 (mt) cc_final: 0.8646 (mt) REVERT: C 356 ARG cc_start: 0.8005 (mtt180) cc_final: 0.6189 (mtm180) REVERT: C 367 ASP cc_start: 0.8258 (m-30) cc_final: 0.7982 (m-30) REVERT: C 649 MET cc_start: 0.9042 (tpp) cc_final: 0.8608 (tpp) REVERT: C 682 PHE cc_start: 0.7869 (p90) cc_final: 0.7476 (p90) REVERT: D 421 LYS cc_start: 0.9392 (pptt) cc_final: 0.8816 (mmtt) REVERT: D 566 GLN cc_start: 0.7827 (mt0) cc_final: 0.7306 (mp-120) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1300 time to fit residues: 40.6074 Evaluate side-chains 171 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN D 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.105739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079354 restraints weight = 48851.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080359 restraints weight = 38494.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080598 restraints weight = 29137.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080817 restraints weight = 23762.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080970 restraints weight = 21617.789| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15038 Z= 0.140 Angle : 0.601 9.192 20409 Z= 0.309 Chirality : 0.043 0.252 2198 Planarity : 0.004 0.043 2584 Dihedral : 5.519 57.999 2276 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.21), residues: 1761 helix: 1.03 (0.19), residues: 828 sheet: -0.32 (0.55), residues: 106 loop : -1.53 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 176 TYR 0.021 0.001 TYR D 446 PHE 0.016 0.001 PHE A 515 TRP 0.028 0.001 TRP C 162 HIS 0.005 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00304 (15008) covalent geometry : angle 0.59156 (20333) SS BOND : bond 0.00363 ( 14) SS BOND : angle 0.91398 ( 28) hydrogen bonds : bond 0.04506 ( 622) hydrogen bonds : angle 4.75916 ( 1746) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 1.44775 ( 12) link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.42223 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8720 (m-30) cc_final: 0.8439 (t70) REVERT: A 366 ASP cc_start: 0.8105 (p0) cc_final: 0.7862 (p0) REVERT: A 375 MET cc_start: 0.8857 (ttt) cc_final: 0.8576 (ttt) REVERT: A 607 ASP cc_start: 0.8383 (p0) cc_final: 0.7893 (p0) REVERT: A 649 MET cc_start: 0.8752 (mmm) cc_final: 0.8510 (mmm) REVERT: C 67 ASN cc_start: 0.9432 (p0) cc_final: 0.9224 (p0) REVERT: C 222 MET cc_start: 0.8323 (mpp) cc_final: 0.7622 (mpp) REVERT: C 248 MET cc_start: 0.8499 (ppp) cc_final: 0.8130 (ppp) REVERT: C 350 LEU cc_start: 0.8698 (mt) cc_final: 0.8484 (mt) REVERT: C 356 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7191 (mtm-85) REVERT: C 366 ASP cc_start: 0.8118 (p0) cc_final: 0.7447 (p0) REVERT: C 367 ASP cc_start: 0.8568 (m-30) cc_final: 0.8191 (m-30) REVERT: C 607 ASP cc_start: 0.8335 (p0) cc_final: 0.7849 (p0) REVERT: C 649 MET cc_start: 0.8810 (tpp) cc_final: 0.8389 (tpp) REVERT: C 682 PHE cc_start: 0.7818 (p90) cc_final: 0.7538 (p90) REVERT: D 421 LYS cc_start: 0.9301 (pptt) cc_final: 0.8691 (mmtt) outliers start: 2 outliers final: 0 residues processed: 214 average time/residue: 0.1207 time to fit residues: 39.0249 Evaluate side-chains 168 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081857 restraints weight = 47012.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081449 restraints weight = 31079.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082307 restraints weight = 24675.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.082730 restraints weight = 22216.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082755 restraints weight = 18997.190| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15038 Z= 0.126 Angle : 0.589 9.271 20409 Z= 0.302 Chirality : 0.042 0.252 2198 Planarity : 0.004 0.050 2584 Dihedral : 5.586 58.438 2276 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.21), residues: 1761 helix: 0.97 (0.18), residues: 828 sheet: -0.62 (0.52), residues: 121 loop : -1.47 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 530 TYR 0.026 0.001 TYR B 456 PHE 0.034 0.001 PHE A 463 TRP 0.029 0.001 TRP C 162 HIS 0.011 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00272 (15008) covalent geometry : angle 0.58043 (20333) SS BOND : bond 0.00561 ( 14) SS BOND : angle 0.79721 ( 28) hydrogen bonds : bond 0.04269 ( 622) hydrogen bonds : angle 4.53713 ( 1746) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 1.35728 ( 12) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.34168 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8817 (m-30) cc_final: 0.8456 (t70) REVERT: A 366 ASP cc_start: 0.8068 (p0) cc_final: 0.7565 (p0) REVERT: A 367 ASP cc_start: 0.8353 (m-30) cc_final: 0.8027 (m-30) REVERT: A 649 MET cc_start: 0.8721 (mmm) cc_final: 0.8398 (tpp) REVERT: B 566 GLN cc_start: 0.7529 (mp-120) cc_final: 0.7290 (mm-40) REVERT: C 222 MET cc_start: 0.8398 (mpp) cc_final: 0.7632 (mpp) REVERT: C 248 MET cc_start: 0.8403 (ppp) cc_final: 0.8037 (ppp) REVERT: C 356 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7132 (mtm-85) REVERT: C 367 ASP cc_start: 0.8527 (m-30) cc_final: 0.8244 (m-30) REVERT: C 607 ASP cc_start: 0.8250 (p0) cc_final: 0.7817 (p0) REVERT: C 649 MET cc_start: 0.8839 (tpp) cc_final: 0.8447 (tpp) REVERT: C 682 PHE cc_start: 0.7782 (p90) cc_final: 0.7467 (p90) REVERT: D 421 LYS cc_start: 0.9339 (pptt) cc_final: 0.8763 (mmtt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1314 time to fit residues: 43.0955 Evaluate side-chains 170 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 106 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 127 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN C 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080379 restraints weight = 47382.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081592 restraints weight = 33317.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082049 restraints weight = 22726.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082335 restraints weight = 22252.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082519 restraints weight = 19826.441| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15038 Z= 0.120 Angle : 0.578 9.381 20409 Z= 0.295 Chirality : 0.042 0.252 2198 Planarity : 0.004 0.053 2584 Dihedral : 5.609 58.545 2276 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.21), residues: 1761 helix: 1.04 (0.19), residues: 816 sheet: -0.72 (0.50), residues: 123 loop : -1.33 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.001 TYR D 446 PHE 0.018 0.001 PHE A 28 TRP 0.031 0.001 TRP C 162 HIS 0.007 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00260 (15008) covalent geometry : angle 0.56841 (20333) SS BOND : bond 0.00444 ( 14) SS BOND : angle 0.97032 ( 28) hydrogen bonds : bond 0.03982 ( 622) hydrogen bonds : angle 4.41871 ( 1746) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 1.33219 ( 12) link_NAG-ASN : bond 0.00567 ( 12) link_NAG-ASN : angle 2.36199 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8862 (m-30) cc_final: 0.8492 (t70) REVERT: A 322 MET cc_start: 0.7665 (mtt) cc_final: 0.7421 (mtt) REVERT: A 366 ASP cc_start: 0.8020 (p0) cc_final: 0.7240 (p0) REVERT: A 367 ASP cc_start: 0.8362 (m-30) cc_final: 0.7949 (m-30) REVERT: A 649 MET cc_start: 0.8815 (mmm) cc_final: 0.8524 (tpp) REVERT: B 421 LYS cc_start: 0.9343 (pptt) cc_final: 0.8726 (mmtt) REVERT: C 222 MET cc_start: 0.8400 (mpp) cc_final: 0.7507 (mpp) REVERT: C 350 LEU cc_start: 0.8904 (mt) cc_final: 0.8616 (mt) REVERT: C 356 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7050 (mtm-85) REVERT: C 366 ASP cc_start: 0.8049 (p0) cc_final: 0.7344 (p0) REVERT: C 367 ASP cc_start: 0.8504 (m-30) cc_final: 0.8071 (m-30) REVERT: C 682 PHE cc_start: 0.7797 (p90) cc_final: 0.7499 (p90) REVERT: D 421 LYS cc_start: 0.9369 (pptt) cc_final: 0.8796 (mmtt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1284 time to fit residues: 42.6422 Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 130 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS C 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.109390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081328 restraints weight = 46909.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082544 restraints weight = 30936.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083974 restraints weight = 20831.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084045 restraints weight = 18231.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084182 restraints weight = 16614.476| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15038 Z= 0.114 Angle : 0.605 12.729 20409 Z= 0.304 Chirality : 0.042 0.257 2198 Planarity : 0.003 0.051 2584 Dihedral : 5.629 58.391 2276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.10 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1761 helix: 0.96 (0.19), residues: 824 sheet: -0.77 (0.50), residues: 123 loop : -1.29 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.014 0.001 TYR D 446 PHE 0.027 0.001 PHE C 653 TRP 0.033 0.001 TRP A 162 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00240 (15008) covalent geometry : angle 0.59191 (20333) SS BOND : bond 0.00396 ( 14) SS BOND : angle 2.17849 ( 28) hydrogen bonds : bond 0.03801 ( 622) hydrogen bonds : angle 4.36642 ( 1746) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 1.37632 ( 12) link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 2.24703 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.7808 (t80) cc_final: 0.7597 (t80) REVERT: A 226 ASP cc_start: 0.8858 (m-30) cc_final: 0.8467 (t70) REVERT: A 331 MET cc_start: 0.7627 (tpt) cc_final: 0.7011 (tpp) REVERT: A 366 ASP cc_start: 0.8000 (p0) cc_final: 0.7713 (p0) REVERT: B 421 LYS cc_start: 0.9374 (pptt) cc_final: 0.8734 (mmtt) REVERT: B 460 MET cc_start: 0.8424 (mpp) cc_final: 0.8219 (mpp) REVERT: C 222 MET cc_start: 0.8331 (mpp) cc_final: 0.7498 (mpp) REVERT: C 350 LEU cc_start: 0.8839 (mt) cc_final: 0.8588 (mt) REVERT: C 356 ARG cc_start: 0.7797 (mtt180) cc_final: 0.6991 (mtm-85) REVERT: C 366 ASP cc_start: 0.8047 (p0) cc_final: 0.7316 (p0) REVERT: C 367 ASP cc_start: 0.8467 (m-30) cc_final: 0.8072 (m-30) REVERT: C 607 ASP cc_start: 0.8226 (p0) cc_final: 0.7690 (p0) REVERT: C 682 PHE cc_start: 0.7857 (p90) cc_final: 0.7474 (p90) REVERT: D 421 LYS cc_start: 0.9406 (pptt) cc_final: 0.8840 (mmtt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1247 time to fit residues: 42.3472 Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 142 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS B 566 GLN C 158 HIS D 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.107414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080325 restraints weight = 47416.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079631 restraints weight = 35328.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080531 restraints weight = 26888.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081055 restraints weight = 23949.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081069 restraints weight = 20927.306| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15038 Z= 0.137 Angle : 0.611 9.349 20409 Z= 0.309 Chirality : 0.043 0.246 2198 Planarity : 0.004 0.053 2584 Dihedral : 5.677 58.798 2276 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.61 % Favored : 92.33 % Rotamer: Outliers : 0.13 % Allowed : 2.58 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.21), residues: 1761 helix: 0.95 (0.19), residues: 824 sheet: -0.73 (0.51), residues: 121 loop : -1.33 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.018 0.001 TYR D 446 PHE 0.025 0.001 PHE A 326 TRP 0.036 0.002 TRP C 162 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00304 (15008) covalent geometry : angle 0.59956 (20333) SS BOND : bond 0.00374 ( 14) SS BOND : angle 1.98906 ( 28) hydrogen bonds : bond 0.03967 ( 622) hydrogen bonds : angle 4.40097 ( 1746) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 1.35787 ( 12) link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 2.24499 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8946 (m-30) cc_final: 0.8545 (t70) REVERT: A 248 MET cc_start: 0.8496 (ppp) cc_final: 0.8276 (ppp) REVERT: A 331 MET cc_start: 0.7674 (tpt) cc_final: 0.7067 (tpp) REVERT: A 366 ASP cc_start: 0.8046 (p0) cc_final: 0.7521 (p0) REVERT: A 367 ASP cc_start: 0.8502 (m-30) cc_final: 0.8193 (m-30) REVERT: A 382 MET cc_start: 0.8365 (mtm) cc_final: 0.8075 (mtp) REVERT: A 607 ASP cc_start: 0.8505 (p0) cc_final: 0.8214 (p0) REVERT: A 649 MET cc_start: 0.8841 (tpp) cc_final: 0.8598 (tpp) REVERT: B 421 LYS cc_start: 0.9376 (pptt) cc_final: 0.8752 (mmtt) REVERT: B 460 MET cc_start: 0.8410 (mpp) cc_final: 0.8143 (mpp) REVERT: C 74 LYS cc_start: 0.9631 (pptt) cc_final: 0.9370 (mmmt) REVERT: C 222 MET cc_start: 0.8399 (mpp) cc_final: 0.7533 (mpp) REVERT: C 350 LEU cc_start: 0.8870 (mt) cc_final: 0.8622 (mt) REVERT: C 356 ARG cc_start: 0.7784 (mtt180) cc_final: 0.6968 (mtm-85) REVERT: C 366 ASP cc_start: 0.8097 (p0) cc_final: 0.7376 (p0) REVERT: C 367 ASP cc_start: 0.8530 (m-30) cc_final: 0.8075 (m-30) REVERT: C 649 MET cc_start: 0.9004 (tpp) cc_final: 0.8662 (tpp) REVERT: C 682 PHE cc_start: 0.7849 (p90) cc_final: 0.7370 (p90) REVERT: D 421 LYS cc_start: 0.9396 (pptt) cc_final: 0.8831 (mmtt) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.1223 time to fit residues: 40.8376 Evaluate side-chains 170 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS B 389 GLN C 158 HIS D 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.108069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081063 restraints weight = 47401.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080660 restraints weight = 33606.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081514 restraints weight = 25949.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081949 restraints weight = 23299.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081976 restraints weight = 19730.335| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15038 Z= 0.126 Angle : 0.617 9.279 20409 Z= 0.311 Chirality : 0.042 0.254 2198 Planarity : 0.004 0.052 2584 Dihedral : 5.698 58.369 2276 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 0.13 % Allowed : 1.70 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.21), residues: 1761 helix: 0.94 (0.19), residues: 824 sheet: -0.65 (0.52), residues: 115 loop : -1.34 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 356 TYR 0.020 0.001 TYR A 73 PHE 0.024 0.001 PHE A 28 TRP 0.039 0.001 TRP C 162 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00277 (15008) covalent geometry : angle 0.60410 (20333) SS BOND : bond 0.00665 ( 14) SS BOND : angle 2.33813 ( 28) hydrogen bonds : bond 0.03933 ( 622) hydrogen bonds : angle 4.36304 ( 1746) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.35597 ( 12) link_NAG-ASN : bond 0.00369 ( 12) link_NAG-ASN : angle 2.22467 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8888 (m-30) cc_final: 0.8507 (t70) REVERT: A 291 ASP cc_start: 0.8415 (t0) cc_final: 0.8176 (p0) REVERT: A 331 MET cc_start: 0.7719 (tpt) cc_final: 0.7161 (tpp) REVERT: A 366 ASP cc_start: 0.8041 (p0) cc_final: 0.7500 (p0) REVERT: A 367 ASP cc_start: 0.8403 (m-30) cc_final: 0.8067 (m-30) REVERT: B 421 LYS cc_start: 0.9376 (pptt) cc_final: 0.8754 (mmtt) REVERT: C 74 LYS cc_start: 0.9621 (pptt) cc_final: 0.9368 (mmmt) REVERT: C 222 MET cc_start: 0.8409 (mpp) cc_final: 0.7528 (mpp) REVERT: C 331 MET cc_start: 0.7429 (tpt) cc_final: 0.7226 (tpt) REVERT: C 367 ASP cc_start: 0.8535 (m-30) cc_final: 0.8220 (m-30) REVERT: C 497 CYS cc_start: 0.8264 (t) cc_final: 0.7995 (m) REVERT: C 682 PHE cc_start: 0.7818 (p90) cc_final: 0.7227 (p90) REVERT: D 421 LYS cc_start: 0.9374 (pptt) cc_final: 0.8801 (mmtt) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1203 time to fit residues: 40.7645 Evaluate side-chains 170 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.0050 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 158 HIS C 588 ASN D 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080571 restraints weight = 47287.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081181 restraints weight = 32850.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082882 restraints weight = 22700.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082962 restraints weight = 19204.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083122 restraints weight = 17724.010| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15038 Z= 0.112 Angle : 0.611 9.342 20409 Z= 0.306 Chirality : 0.042 0.251 2198 Planarity : 0.003 0.049 2584 Dihedral : 5.674 58.024 2276 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 0.13 % Allowed : 0.94 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.21), residues: 1761 helix: 0.94 (0.19), residues: 824 sheet: -0.79 (0.50), residues: 115 loop : -1.30 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 356 TYR 0.018 0.001 TYR A 73 PHE 0.040 0.001 PHE A 463 TRP 0.041 0.001 TRP C 162 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00236 (15008) covalent geometry : angle 0.60009 (20333) SS BOND : bond 0.00291 ( 14) SS BOND : angle 1.97431 ( 28) hydrogen bonds : bond 0.03702 ( 622) hydrogen bonds : angle 4.23266 ( 1746) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.34079 ( 12) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.15204 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8873 (m-30) cc_final: 0.8495 (t70) REVERT: A 331 MET cc_start: 0.7754 (tpt) cc_final: 0.7155 (tpp) REVERT: A 366 ASP cc_start: 0.8041 (p0) cc_final: 0.7486 (p0) REVERT: A 367 ASP cc_start: 0.8394 (m-30) cc_final: 0.8063 (m-30) REVERT: A 607 ASP cc_start: 0.8399 (p0) cc_final: 0.8005 (p0) REVERT: A 649 MET cc_start: 0.8717 (tpp) cc_final: 0.8455 (tpp) REVERT: B 421 LYS cc_start: 0.9366 (pptt) cc_final: 0.8723 (mmtt) REVERT: B 460 MET cc_start: 0.8506 (mpp) cc_final: 0.8231 (mpp) REVERT: C 67 ASN cc_start: 0.9419 (p0) cc_final: 0.9213 (p0) REVERT: C 74 LYS cc_start: 0.9634 (pptt) cc_final: 0.9356 (mmmt) REVERT: C 222 MET cc_start: 0.8314 (mpp) cc_final: 0.7413 (mpp) REVERT: C 331 MET cc_start: 0.7339 (tpt) cc_final: 0.7130 (tpt) REVERT: C 367 ASP cc_start: 0.8442 (m-30) cc_final: 0.8120 (m-30) REVERT: C 497 CYS cc_start: 0.8117 (t) cc_final: 0.7872 (m) REVERT: C 607 ASP cc_start: 0.8223 (p0) cc_final: 0.7620 (p0) REVERT: C 682 PHE cc_start: 0.7788 (p90) cc_final: 0.7212 (p90) REVERT: D 421 LYS cc_start: 0.9381 (pptt) cc_final: 0.8805 (mmtt) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 0.1251 time to fit residues: 40.8095 Evaluate side-chains 174 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 158 HIS D 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.107701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080680 restraints weight = 47574.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081352 restraints weight = 34031.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081770 restraints weight = 26520.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.081919 restraints weight = 22883.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082129 restraints weight = 20594.593| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15038 Z= 0.139 Angle : 0.636 9.226 20409 Z= 0.320 Chirality : 0.043 0.272 2198 Planarity : 0.004 0.048 2584 Dihedral : 5.695 58.547 2276 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.62 % Rotamer: Outliers : 0.13 % Allowed : 0.44 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.21), residues: 1761 helix: 0.97 (0.19), residues: 816 sheet: -0.82 (0.50), residues: 115 loop : -1.36 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 356 TYR 0.024 0.001 TYR A 220 PHE 0.024 0.002 PHE A 28 TRP 0.043 0.002 TRP C 162 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00307 (15008) covalent geometry : angle 0.62200 (20333) SS BOND : bond 0.00325 ( 14) SS BOND : angle 1.93162 ( 28) hydrogen bonds : bond 0.03986 ( 622) hydrogen bonds : angle 4.42641 ( 1746) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 1.37203 ( 12) link_NAG-ASN : bond 0.00948 ( 12) link_NAG-ASN : angle 2.71288 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8254 (mmm) cc_final: 0.7702 (mmm) REVERT: A 331 MET cc_start: 0.7760 (tpt) cc_final: 0.7230 (tpp) REVERT: A 607 ASP cc_start: 0.8482 (p0) cc_final: 0.8136 (p0) REVERT: B 421 LYS cc_start: 0.9286 (pptt) cc_final: 0.8639 (mmtt) REVERT: B 460 MET cc_start: 0.8442 (mpp) cc_final: 0.8222 (mpp) REVERT: C 67 ASN cc_start: 0.9397 (p0) cc_final: 0.9194 (p0) REVERT: C 74 LYS cc_start: 0.9632 (pptt) cc_final: 0.9373 (mmmt) REVERT: C 222 MET cc_start: 0.8415 (mpp) cc_final: 0.7533 (mpp) REVERT: C 367 ASP cc_start: 0.8458 (m-30) cc_final: 0.8138 (m-30) REVERT: C 607 ASP cc_start: 0.8397 (p0) cc_final: 0.7911 (p0) REVERT: C 682 PHE cc_start: 0.7861 (p90) cc_final: 0.7271 (p90) REVERT: D 421 LYS cc_start: 0.9291 (pptt) cc_final: 0.8695 (mmtt) outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.1173 time to fit residues: 37.7724 Evaluate side-chains 163 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 40 optimal weight: 0.0570 chunk 135 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 389 GLN C 158 HIS D 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082765 restraints weight = 47308.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083873 restraints weight = 33971.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084509 restraints weight = 23677.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084924 restraints weight = 19740.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084976 restraints weight = 18770.607| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15038 Z= 0.115 Angle : 0.625 9.363 20409 Z= 0.313 Chirality : 0.043 0.244 2198 Planarity : 0.003 0.048 2584 Dihedral : 5.659 57.714 2276 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.21), residues: 1761 helix: 0.93 (0.19), residues: 818 sheet: -0.57 (0.51), residues: 107 loop : -1.34 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 356 TYR 0.018 0.001 TYR A 73 PHE 0.025 0.001 PHE A 28 TRP 0.045 0.001 TRP C 162 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00246 (15008) covalent geometry : angle 0.61140 (20333) SS BOND : bond 0.00274 ( 14) SS BOND : angle 1.79688 ( 28) hydrogen bonds : bond 0.03701 ( 622) hydrogen bonds : angle 4.33254 ( 1746) link_BETA1-4 : bond 0.00463 ( 4) link_BETA1-4 : angle 1.34819 ( 12) link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 2.70798 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.608 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: A 226 ASP cc_start: 0.8845 (m-30) cc_final: 0.8581 (t70) REVERT: A 331 MET cc_start: 0.7698 (tpt) cc_final: 0.7204 (tpp) REVERT: A 382 MET cc_start: 0.8548 (mtm) cc_final: 0.8273 (mtm) REVERT: A 607 ASP cc_start: 0.8496 (p0) cc_final: 0.8173 (p0) REVERT: A 649 MET cc_start: 0.8639 (tpp) cc_final: 0.8394 (tpp) REVERT: B 421 LYS cc_start: 0.9223 (pptt) cc_final: 0.8572 (mmtt) REVERT: B 460 MET cc_start: 0.8362 (mpp) cc_final: 0.8147 (mpp) REVERT: C 67 ASN cc_start: 0.9355 (p0) cc_final: 0.9147 (p0) REVERT: C 222 MET cc_start: 0.8255 (mpp) cc_final: 0.7397 (mpp) REVERT: C 350 LEU cc_start: 0.8746 (mt) cc_final: 0.8500 (mt) REVERT: C 367 ASP cc_start: 0.8367 (m-30) cc_final: 0.8074 (m-30) REVERT: C 607 ASP cc_start: 0.8374 (p0) cc_final: 0.7855 (p0) REVERT: C 682 PHE cc_start: 0.7818 (p90) cc_final: 0.7287 (p90) REVERT: D 421 LYS cc_start: 0.9211 (pptt) cc_final: 0.8620 (mmtt) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 0.1254 time to fit residues: 40.4720 Evaluate side-chains 177 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 389 GLN C 158 HIS ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.106319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079896 restraints weight = 47561.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081187 restraints weight = 32707.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.081561 restraints weight = 26164.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081587 restraints weight = 20784.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081748 restraints weight = 20458.384| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15038 Z= 0.173 Angle : 0.656 9.558 20409 Z= 0.334 Chirality : 0.044 0.244 2198 Planarity : 0.004 0.050 2584 Dihedral : 5.764 58.867 2276 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer: Outliers : 0.19 % Allowed : 0.50 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1761 helix: 0.92 (0.19), residues: 818 sheet: -0.70 (0.50), residues: 107 loop : -1.48 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.037 0.002 TYR C 73 PHE 0.028 0.002 PHE C 515 TRP 0.037 0.002 TRP C 162 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00389 (15008) covalent geometry : angle 0.64211 (20333) SS BOND : bond 0.00364 ( 14) SS BOND : angle 1.99056 ( 28) hydrogen bonds : bond 0.04283 ( 622) hydrogen bonds : angle 4.55997 ( 1746) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.41097 ( 12) link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.66314 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.53 seconds wall clock time: 43 minutes 43.48 seconds (2623.48 seconds total)