Starting phenix.real_space_refine on Sun Aug 24 07:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm1_19348/08_2025/8rm1_19348.cif" } resolution = 3.1 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= 0.003 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 108 5.16 5 C 11421 2.51 5 N 3015 2.21 5 O 3369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17913 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5890 Classifications: {'peptide': 728} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 5 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, F, H, G, I Time building chain proxies: 5.35, per 1000 atoms: 0.30 Number of scatterers: 17913 At special positions: 0 Unit cell: (131.58, 138.46, 174.58, 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 108 16.00 O 3369 8.00 N 3015 7.00 C 11421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 403 " - pdb=" SG CYS A 483 " distance=2.04 Simple disulfide: pdb=" SG CYS A 417 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 762 " - pdb=" SG CYS A 770 " distance=2.03 Simple disulfide: pdb=" SG CYS A 779 " - pdb=" SG CYS A 788 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 403 " - pdb=" SG CYS B 483 " distance=2.04 Simple disulfide: pdb=" SG CYS C 403 " - pdb=" SG CYS C 483 " distance=2.04 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 417 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 762 " - pdb=" SG CYS B 770 " distance=2.03 Simple disulfide: pdb=" SG CYS C 762 " - pdb=" SG CYS C 770 " distance=2.03 Simple disulfide: pdb=" SG CYS B 779 " - pdb=" SG CYS B 788 " distance=2.03 Simple disulfide: pdb=" SG CYS C 779 " - pdb=" SG CYS C 788 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 837 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG B1001 " - " ASN B 141 " " NAG C1001 " - " ASN C 141 " " NAG D 1 " - " ASN A 183 " " NAG E 1 " - " ASN A 807 " " NAG F 1 " - " ASN B 183 " " NAG G 1 " - " ASN B 807 " " NAG H 1 " - " ASN C 183 " " NAG I 1 " - " ASN C 807 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 771.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 30 sheets defined 32.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 188 through 205 removed outlier: 3.847A pdb=" N MET A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.986A pdb=" N ASP A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.733A pdb=" N LEU A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.636A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.092A pdb=" N ASN A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.929A pdb=" N VAL A 410 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 511 through 524 Processing helix chain 'A' and resid 576 through 651 removed outlier: 3.892A pdb=" N MET A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 587 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 623 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 641 " --> pdb=" O HIS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.573A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 877 removed outlier: 3.834A pdb=" N ILE A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 899 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.847A pdb=" N MET B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.986A pdb=" N ASP B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.734A pdb=" N LEU B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.636A pdb=" N VAL B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.092A pdb=" N ASN B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.929A pdb=" N VAL B 410 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 576 through 651 removed outlier: 3.893A pdb=" N MET B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY B 588 " --> pdb=" O TYR B 584 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 623 " --> pdb=" O MET B 619 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 635 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 641 " --> pdb=" O HIS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 671 through 681 removed outlier: 3.574A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 877 removed outlier: 3.834A pdb=" N ILE B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 899 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 188 through 205 removed outlier: 3.848A pdb=" N MET C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.985A pdb=" N ASP C 274 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.734A pdb=" N LEU C 307 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 347 Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.636A pdb=" N VAL C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.091A pdb=" N ASN C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.929A pdb=" N VAL C 410 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'C' and resid 576 through 651 removed outlier: 3.894A pdb=" N MET C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR C 587 " --> pdb=" O GLY C 583 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C 588 " --> pdb=" O TYR C 584 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 622 " --> pdb=" O LEU C 618 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 623 " --> pdb=" O MET C 619 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 641 " --> pdb=" O HIS C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 671 through 681 removed outlier: 3.574A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 877 removed outlier: 3.834A pdb=" N ILE C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 899 Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.883A pdb=" N LEU A 757 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 775 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 759 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 773 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU A 761 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 771 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 170 removed outlier: 3.855A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 170 removed outlier: 3.855A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 700 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN A 691 " --> pdb=" O ALA A 700 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU A 702 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 689 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 704 " --> pdb=" O TYR A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.574A pdb=" N TRP A 791 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 835 through 837 Processing sheet with id=AB2, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.883A pdb=" N LEU B 757 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 775 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 759 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 773 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU B 761 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 771 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 161 through 170 removed outlier: 3.856A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 170 removed outlier: 3.856A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA B 700 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN B 691 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU B 702 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 689 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 704 " --> pdb=" O TYR B 687 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 495 through 498 Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349 Processing sheet with id=AB9, first strand: chain 'B' and resid 395 through 397 Processing sheet with id=AC1, first strand: chain 'B' and resid 727 through 728 removed outlier: 3.575A pdb=" N TRP B 791 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 835 through 837 Processing sheet with id=AC3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 152 removed outlier: 6.882A pdb=" N LEU C 757 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 775 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 759 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C 773 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU C 761 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 771 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 170 removed outlier: 3.854A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 170 removed outlier: 3.854A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA C 700 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN C 691 " --> pdb=" O ALA C 700 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU C 702 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL C 689 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY C 704 " --> pdb=" O TYR C 687 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 495 through 498 Processing sheet with id=AC8, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC9, first strand: chain 'C' and resid 348 through 349 Processing sheet with id=AD1, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AD2, first strand: chain 'C' and resid 727 through 728 removed outlier: 3.575A pdb=" N TRP C 791 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 835 through 837 654 hydrogen bonds defined for protein. 1737 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: 3.19 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5727 1.34 - 1.46: 4188 1.46 - 1.58: 8262 1.58 - 1.70: 0 1.70 - 1.82: 159 Bond restraints: 18336 Sorted by residual: bond pdb=" CA LEU C 586 " pdb=" C LEU C 586 " ideal model delta sigma weight residual 1.523 1.564 -0.040 1.80e-02 3.09e+03 4.99e+00 bond pdb=" CA LEU A 586 " pdb=" C LEU A 586 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.80e-02 3.09e+03 4.98e+00 bond pdb=" CA LEU B 586 " pdb=" C LEU B 586 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.80e-02 3.09e+03 4.94e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.547 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 18331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 24347 1.95 - 3.90: 478 3.90 - 5.84: 70 5.84 - 7.79: 8 7.79 - 9.74: 12 Bond angle restraints: 24915 Sorted by residual: angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 111.62 109.39 2.23 7.90e-01 1.60e+00 8.00e+00 angle pdb=" N ILE B 489 " pdb=" CA ILE B 489 " pdb=" C ILE B 489 " ideal model delta sigma weight residual 111.62 109.40 2.22 7.90e-01 1.60e+00 7.91e+00 angle pdb=" N ILE C 489 " pdb=" CA ILE C 489 " pdb=" C ILE C 489 " ideal model delta sigma weight residual 111.62 109.41 2.21 7.90e-01 1.60e+00 7.86e+00 angle pdb=" CB MET C 619 " pdb=" CG MET C 619 " pdb=" SD MET C 619 " ideal model delta sigma weight residual 112.70 121.07 -8.37 3.00e+00 1.11e-01 7.78e+00 angle pdb=" CB MET B 619 " pdb=" CG MET B 619 " pdb=" SD MET B 619 " ideal model delta sigma weight residual 112.70 121.07 -8.37 3.00e+00 1.11e-01 7.78e+00 ... (remaining 24910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 10616 21.88 - 43.75: 616 43.75 - 65.63: 105 65.63 - 87.51: 45 87.51 - 109.38: 12 Dihedral angle restraints: 11394 sinusoidal: 4905 harmonic: 6489 Sorted by residual: dihedral pdb=" CB CYS B 779 " pdb=" SG CYS B 779 " pdb=" SG CYS B 788 " pdb=" CB CYS B 788 " ideal model delta sinusoidal sigma weight residual 93.00 178.53 -85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 779 " pdb=" SG CYS A 779 " pdb=" SG CYS A 788 " pdb=" CB CYS A 788 " ideal model delta sinusoidal sigma weight residual 93.00 178.53 -85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS C 779 " pdb=" SG CYS C 779 " pdb=" SG CYS C 788 " pdb=" CB CYS C 788 " ideal model delta sinusoidal sigma weight residual 93.00 178.50 -85.50 1 1.00e+01 1.00e-02 8.85e+01 ... (remaining 11391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2370 0.056 - 0.112: 378 0.112 - 0.169: 66 0.169 - 0.225: 0 0.225 - 0.281: 6 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2817 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 533 " 0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO A 534 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 533 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO C 534 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 534 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 534 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 533 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 534 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 534 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 534 " -0.046 5.00e-02 4.00e+02 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1051 2.74 - 3.28: 16913 3.28 - 3.82: 27189 3.82 - 4.36: 32144 4.36 - 4.90: 56091 Nonbonded interactions: 133388 Sorted by model distance: nonbonded pdb=" O ASN C 718 " pdb=" ND2 ASN C 748 " model vdw 2.195 3.120 nonbonded pdb=" O ASN A 718 " pdb=" ND2 ASN A 748 " model vdw 2.195 3.120 nonbonded pdb=" O ASN B 718 " pdb=" ND2 ASN B 748 " model vdw 2.196 3.120 nonbonded pdb=" ND2 ASN A 724 " pdb=" O LEU A 740 " model vdw 2.243 3.120 nonbonded pdb=" ND2 ASN B 724 " pdb=" O LEU B 740 " model vdw 2.243 3.120 ... (remaining 133383 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 0.040 18381 Z= 0.155 Angle : 0.662 9.740 25023 Z= 0.336 Chirality : 0.044 0.281 2820 Planarity : 0.005 0.085 3153 Dihedral : 14.776 109.384 7125 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.45 % Allowed : 0.61 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.18), residues: 2148 helix: 1.35 (0.21), residues: 648 sheet: 0.12 (0.26), residues: 423 loop : -1.66 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 652 TYR 0.011 0.001 TYR C 688 PHE 0.008 0.001 PHE C 838 TRP 0.009 0.001 TRP C 720 HIS 0.003 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00311 (18336) covalent geometry : angle 0.65882 (24915) SS BOND : bond 0.00195 ( 27) SS BOND : angle 0.78197 ( 54) hydrogen bonds : bond 0.15675 ( 633) hydrogen bonds : angle 6.07897 ( 1737) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.49552 ( 27) link_NAG-ASN : bond 0.00354 ( 9) link_NAG-ASN : angle 1.40187 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.732 Fit side-chains REVERT: A 198 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 248 ASN cc_start: 0.6424 (t0) cc_final: 0.5975 (t0) REVERT: A 521 ASN cc_start: 0.7770 (t0) cc_final: 0.7548 (t0) REVERT: B 198 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: B 248 ASN cc_start: 0.6276 (t0) cc_final: 0.5776 (t0) REVERT: C 198 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: C 248 ASN cc_start: 0.6397 (t0) cc_final: 0.5970 (t0) REVERT: C 899 GLU cc_start: 0.7702 (tp30) cc_final: 0.7250 (tp30) outliers start: 9 outliers final: 0 residues processed: 218 average time/residue: 0.1244 time to fit residues: 42.4119 Evaluate side-chains 172 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.195526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120669 restraints weight = 23266.430| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.47 r_work: 0.3020 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18381 Z= 0.140 Angle : 0.618 12.047 25023 Z= 0.304 Chirality : 0.045 0.250 2820 Planarity : 0.004 0.055 3153 Dihedral : 8.082 64.804 2784 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.36 % Allowed : 4.75 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.49 (0.18), residues: 2148 helix: 1.56 (0.22), residues: 648 sheet: -0.02 (0.26), residues: 411 loop : -1.70 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR C 707 PHE 0.018 0.002 PHE C 517 TRP 0.010 0.001 TRP B 720 HIS 0.003 0.001 HIS C 624 Details of bonding type rmsd covalent geometry : bond 0.00322 (18336) covalent geometry : angle 0.61295 (24915) SS BOND : bond 0.00258 ( 27) SS BOND : angle 0.92583 ( 54) hydrogen bonds : bond 0.05619 ( 633) hydrogen bonds : angle 4.67060 ( 1737) link_BETA1-4 : bond 0.00397 ( 9) link_BETA1-4 : angle 2.00343 ( 27) link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 1.23160 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.742 Fit side-chains REVERT: A 198 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: A 230 GLN cc_start: 0.7321 (mt0) cc_final: 0.7081 (mt0) REVERT: A 248 ASN cc_start: 0.5618 (t0) cc_final: 0.5018 (t0) REVERT: A 521 ASN cc_start: 0.7309 (t0) cc_final: 0.7085 (t0) REVERT: A 651 GLU cc_start: 0.8248 (tp30) cc_final: 0.8047 (tp30) REVERT: A 899 GLU cc_start: 0.8014 (tp30) cc_final: 0.7602 (tp30) REVERT: B 198 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8463 (pt0) REVERT: B 230 GLN cc_start: 0.7206 (mt0) cc_final: 0.6945 (mt0) REVERT: B 248 ASN cc_start: 0.5553 (t0) cc_final: 0.4908 (t0) REVERT: B 298 MET cc_start: 0.5881 (tpt) cc_final: 0.5666 (tpt) REVERT: B 384 GLU cc_start: 0.7287 (mp0) cc_final: 0.7064 (mp0) REVERT: C 140 VAL cc_start: 0.7548 (m) cc_final: 0.7187 (t) REVERT: C 198 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: C 248 ASN cc_start: 0.5724 (t0) cc_final: 0.5169 (t0) REVERT: C 315 ILE cc_start: 0.6517 (mm) cc_final: 0.6250 (mt) outliers start: 27 outliers final: 13 residues processed: 198 average time/residue: 0.1277 time to fit residues: 38.7948 Evaluate side-chains 191 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 584 TYR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 36 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 141 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.196735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122445 restraints weight = 23586.437| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.41 r_work: 0.3073 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18381 Z= 0.106 Angle : 0.560 11.822 25023 Z= 0.273 Chirality : 0.043 0.251 2820 Planarity : 0.004 0.046 3153 Dihedral : 6.497 59.065 2784 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.21 % Allowed : 6.87 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.42 (0.18), residues: 2148 helix: 1.69 (0.22), residues: 648 sheet: -0.05 (0.26), residues: 411 loop : -1.67 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 226 TYR 0.012 0.001 TYR B 707 PHE 0.018 0.001 PHE B 517 TRP 0.007 0.001 TRP B 720 HIS 0.002 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00223 (18336) covalent geometry : angle 0.55552 (24915) SS BOND : bond 0.00203 ( 27) SS BOND : angle 0.82628 ( 54) hydrogen bonds : bond 0.04950 ( 633) hydrogen bonds : angle 4.38817 ( 1737) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.94688 ( 27) link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 1.09388 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.533 Fit side-chains REVERT: A 198 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: A 230 GLN cc_start: 0.7265 (mt0) cc_final: 0.6953 (mt0) REVERT: A 248 ASN cc_start: 0.5417 (t0) cc_final: 0.4944 (t0) REVERT: A 346 ASN cc_start: 0.6387 (t0) cc_final: 0.6123 (t0) REVERT: A 384 GLU cc_start: 0.7555 (mp0) cc_final: 0.7285 (mp0) REVERT: A 521 ASN cc_start: 0.7260 (t0) cc_final: 0.7025 (t0) REVERT: A 899 GLU cc_start: 0.7998 (tp30) cc_final: 0.7546 (tp30) REVERT: B 198 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: B 230 GLN cc_start: 0.7100 (mt0) cc_final: 0.6842 (mt0) REVERT: B 248 ASN cc_start: 0.5419 (t0) cc_final: 0.4953 (t0) REVERT: B 384 GLU cc_start: 0.7272 (mp0) cc_final: 0.7030 (mp0) REVERT: C 140 VAL cc_start: 0.7382 (m) cc_final: 0.7163 (t) REVERT: C 198 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: C 248 ASN cc_start: 0.5535 (t0) cc_final: 0.4919 (t0) REVERT: C 315 ILE cc_start: 0.6622 (mm) cc_final: 0.6361 (mt) outliers start: 24 outliers final: 10 residues processed: 193 average time/residue: 0.1262 time to fit residues: 37.8884 Evaluate side-chains 181 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.193818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118285 restraints weight = 23359.039| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.37 r_work: 0.3000 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18381 Z= 0.141 Angle : 0.601 12.308 25023 Z= 0.295 Chirality : 0.045 0.236 2820 Planarity : 0.004 0.056 3153 Dihedral : 5.964 59.359 2784 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.46 % Allowed : 9.04 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.53 (0.18), residues: 2148 helix: 1.66 (0.21), residues: 648 sheet: -0.18 (0.25), residues: 411 loop : -1.76 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 646 TYR 0.017 0.001 TYR C 707 PHE 0.019 0.002 PHE C 517 TRP 0.009 0.001 TRP B 720 HIS 0.004 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00332 (18336) covalent geometry : angle 0.59649 (24915) SS BOND : bond 0.00203 ( 27) SS BOND : angle 0.85776 ( 54) hydrogen bonds : bond 0.05641 ( 633) hydrogen bonds : angle 4.40175 ( 1737) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.82212 ( 27) link_NAG-ASN : bond 0.00313 ( 9) link_NAG-ASN : angle 1.23829 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.484 Fit side-chains REVERT: A 198 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 230 GLN cc_start: 0.7309 (mt0) cc_final: 0.6998 (mt0) REVERT: A 248 ASN cc_start: 0.5525 (t0) cc_final: 0.5089 (t0) REVERT: A 298 MET cc_start: 0.5515 (tpt) cc_final: 0.5271 (tpt) REVERT: A 899 GLU cc_start: 0.7948 (tp30) cc_final: 0.7437 (tp30) REVERT: B 198 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: B 230 GLN cc_start: 0.7128 (mt0) cc_final: 0.6882 (mt0) REVERT: B 248 ASN cc_start: 0.5542 (t0) cc_final: 0.5061 (t0) REVERT: B 384 GLU cc_start: 0.7359 (mp0) cc_final: 0.7114 (mp0) REVERT: C 140 VAL cc_start: 0.7480 (m) cc_final: 0.7229 (t) REVERT: C 198 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: C 248 ASN cc_start: 0.5602 (t0) cc_final: 0.5028 (t0) REVERT: C 315 ILE cc_start: 0.6755 (mm) cc_final: 0.6508 (mt) outliers start: 29 outliers final: 14 residues processed: 188 average time/residue: 0.1288 time to fit residues: 37.5928 Evaluate side-chains 181 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 133 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.195009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121852 restraints weight = 23303.141| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.57 r_work: 0.2967 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18381 Z= 0.119 Angle : 0.577 10.627 25023 Z= 0.281 Chirality : 0.044 0.237 2820 Planarity : 0.004 0.050 3153 Dihedral : 5.761 59.940 2784 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.16 % Allowed : 10.05 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.53 (0.18), residues: 2148 helix: 1.71 (0.22), residues: 648 sheet: -0.24 (0.25), residues: 411 loop : -1.76 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 283 TYR 0.014 0.001 TYR C 707 PHE 0.019 0.001 PHE B 517 TRP 0.008 0.001 TRP A 701 HIS 0.003 0.001 HIS C 624 Details of bonding type rmsd covalent geometry : bond 0.00268 (18336) covalent geometry : angle 0.57290 (24915) SS BOND : bond 0.00199 ( 27) SS BOND : angle 0.84603 ( 54) hydrogen bonds : bond 0.05245 ( 633) hydrogen bonds : angle 4.28981 ( 1737) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 1.67062 ( 27) link_NAG-ASN : bond 0.00331 ( 9) link_NAG-ASN : angle 1.15543 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.707 Fit side-chains REVERT: A 230 GLN cc_start: 0.7293 (mt0) cc_final: 0.7002 (mt0) REVERT: A 248 ASN cc_start: 0.5524 (t0) cc_final: 0.5068 (t0) REVERT: A 298 MET cc_start: 0.5710 (tpt) cc_final: 0.5480 (tpt) REVERT: A 579 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 899 GLU cc_start: 0.7986 (tp30) cc_final: 0.7747 (tp30) REVERT: B 230 GLN cc_start: 0.7211 (mt0) cc_final: 0.6966 (mt0) REVERT: B 248 ASN cc_start: 0.5626 (t0) cc_final: 0.5137 (t0) REVERT: C 140 VAL cc_start: 0.7582 (m) cc_final: 0.7294 (t) REVERT: C 198 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: C 248 ASN cc_start: 0.5615 (t0) cc_final: 0.5005 (t0) REVERT: C 315 ILE cc_start: 0.6791 (mm) cc_final: 0.6527 (mt) REVERT: C 578 LYS cc_start: 0.6681 (ptpp) cc_final: 0.5617 (pttt) outliers start: 23 outliers final: 15 residues processed: 183 average time/residue: 0.1426 time to fit residues: 40.0695 Evaluate side-chains 178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 584 TYR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 0.0170 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 0.0570 chunk 80 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.193982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120122 restraints weight = 23255.688| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.47 r_work: 0.3046 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18381 Z= 0.120 Angle : 0.578 10.642 25023 Z= 0.281 Chirality : 0.044 0.236 2820 Planarity : 0.004 0.049 3153 Dihedral : 5.516 59.189 2778 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.62 % Allowed : 10.25 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.54 (0.18), residues: 2148 helix: 1.72 (0.21), residues: 648 sheet: -0.32 (0.25), residues: 429 loop : -1.77 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 283 TYR 0.015 0.001 TYR B 707 PHE 0.020 0.001 PHE B 517 TRP 0.007 0.001 TRP A 701 HIS 0.003 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00273 (18336) covalent geometry : angle 0.57394 (24915) SS BOND : bond 0.00193 ( 27) SS BOND : angle 0.81719 ( 54) hydrogen bonds : bond 0.05240 ( 633) hydrogen bonds : angle 4.25859 ( 1737) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.64071 ( 27) link_NAG-ASN : bond 0.00326 ( 9) link_NAG-ASN : angle 1.20203 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.484 Fit side-chains REVERT: A 248 ASN cc_start: 0.5480 (t0) cc_final: 0.5049 (t0) REVERT: A 899 GLU cc_start: 0.7939 (tp30) cc_final: 0.7677 (tp30) REVERT: B 140 VAL cc_start: 0.7560 (m) cc_final: 0.7320 (t) REVERT: B 142 MET cc_start: 0.8258 (mtt) cc_final: 0.8038 (mtt) REVERT: B 230 GLN cc_start: 0.7210 (mt0) cc_final: 0.6977 (mt0) REVERT: B 248 ASN cc_start: 0.5609 (t0) cc_final: 0.5155 (t0) REVERT: B 384 GLU cc_start: 0.7473 (mp0) cc_final: 0.7218 (mp0) REVERT: B 579 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8004 (tt) REVERT: C 140 VAL cc_start: 0.7576 (m) cc_final: 0.7366 (t) REVERT: C 248 ASN cc_start: 0.5587 (t0) cc_final: 0.4989 (t0) REVERT: C 315 ILE cc_start: 0.6805 (mm) cc_final: 0.6481 (mt) REVERT: C 578 LYS cc_start: 0.6756 (ptpp) cc_final: 0.5752 (pttt) REVERT: C 579 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7880 (tt) outliers start: 32 outliers final: 17 residues processed: 190 average time/residue: 0.1280 time to fit residues: 36.9850 Evaluate side-chains 179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 171 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 595 GLN B 591 GLN B 595 GLN C 591 GLN C 595 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113710 restraints weight = 23339.360| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.47 r_work: 0.2925 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 18381 Z= 0.324 Angle : 0.812 10.624 25023 Z= 0.407 Chirality : 0.054 0.258 2820 Planarity : 0.006 0.078 3153 Dihedral : 6.134 58.957 2775 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.67 % Allowed : 10.81 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.31 (0.17), residues: 2148 helix: 0.78 (0.21), residues: 678 sheet: -0.63 (0.24), residues: 429 loop : -2.17 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 163 TYR 0.023 0.002 TYR C 707 PHE 0.021 0.003 PHE C 842 TRP 0.011 0.002 TRP B 701 HIS 0.007 0.002 HIS C 624 Details of bonding type rmsd covalent geometry : bond 0.00825 (18336) covalent geometry : angle 0.80531 (24915) SS BOND : bond 0.00362 ( 27) SS BOND : angle 1.16847 ( 54) hydrogen bonds : bond 0.08155 ( 633) hydrogen bonds : angle 4.74407 ( 1737) link_BETA1-4 : bond 0.00500 ( 9) link_BETA1-4 : angle 2.45341 ( 27) link_NAG-ASN : bond 0.00237 ( 9) link_NAG-ASN : angle 1.79089 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.465 Fit side-chains REVERT: A 230 GLN cc_start: 0.7459 (mt0) cc_final: 0.7102 (mt0) REVERT: A 248 ASN cc_start: 0.5722 (t0) cc_final: 0.5403 (t0) REVERT: A 309 ASN cc_start: 0.6900 (m110) cc_final: 0.6664 (m-40) REVERT: A 505 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7440 (mt) REVERT: A 895 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: A 899 GLU cc_start: 0.7845 (tp30) cc_final: 0.7509 (tp30) REVERT: B 230 GLN cc_start: 0.7284 (mt0) cc_final: 0.7061 (mt0) REVERT: B 248 ASN cc_start: 0.5692 (t0) cc_final: 0.5249 (t0) REVERT: B 309 ASN cc_start: 0.6852 (m110) cc_final: 0.6596 (m-40) REVERT: B 384 GLU cc_start: 0.7556 (mp0) cc_final: 0.7263 (mp0) REVERT: B 505 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7451 (mt) REVERT: C 315 ILE cc_start: 0.6889 (mm) cc_final: 0.6676 (mt) REVERT: C 505 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7421 (mt) REVERT: C 578 LYS cc_start: 0.6886 (ptpp) cc_final: 0.5847 (pttt) REVERT: C 579 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8023 (tt) REVERT: C 751 CYS cc_start: 0.8988 (t) cc_final: 0.8613 (t) outliers start: 33 outliers final: 18 residues processed: 181 average time/residue: 0.1232 time to fit residues: 34.2223 Evaluate side-chains 178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 895 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 171 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.193991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119963 restraints weight = 23243.733| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.44 r_work: 0.2976 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18381 Z= 0.131 Angle : 0.617 10.103 25023 Z= 0.301 Chirality : 0.044 0.245 2820 Planarity : 0.005 0.061 3153 Dihedral : 5.424 58.000 2775 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.16 % Allowed : 11.16 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.96 (0.18), residues: 2148 helix: 1.31 (0.21), residues: 666 sheet: -0.49 (0.25), residues: 429 loop : -2.07 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 652 TYR 0.016 0.001 TYR B 707 PHE 0.022 0.001 PHE C 517 TRP 0.016 0.001 TRP B 399 HIS 0.003 0.001 HIS C 867 Details of bonding type rmsd covalent geometry : bond 0.00301 (18336) covalent geometry : angle 0.61173 (24915) SS BOND : bond 0.00233 ( 27) SS BOND : angle 1.01254 ( 54) hydrogen bonds : bond 0.05617 ( 633) hydrogen bonds : angle 4.43793 ( 1737) link_BETA1-4 : bond 0.00451 ( 9) link_BETA1-4 : angle 1.82450 ( 27) link_NAG-ASN : bond 0.00424 ( 9) link_NAG-ASN : angle 1.36216 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.612 Fit side-chains REVERT: A 248 ASN cc_start: 0.5550 (t0) cc_final: 0.5156 (t0) REVERT: A 298 MET cc_start: 0.5782 (tpt) cc_final: 0.5395 (tpt) REVERT: A 309 ASN cc_start: 0.6688 (m110) cc_final: 0.6441 (m-40) REVERT: A 899 GLU cc_start: 0.7789 (tp30) cc_final: 0.7420 (tp30) REVERT: B 230 GLN cc_start: 0.7191 (mt0) cc_final: 0.6964 (mt0) REVERT: B 248 ASN cc_start: 0.5649 (t0) cc_final: 0.5198 (t0) REVERT: B 292 LEU cc_start: 0.1632 (OUTLIER) cc_final: 0.1380 (mm) REVERT: B 309 ASN cc_start: 0.6620 (m110) cc_final: 0.6358 (m-40) REVERT: B 384 GLU cc_start: 0.7544 (mp0) cc_final: 0.7300 (mp0) REVERT: C 248 ASN cc_start: 0.5714 (t0) cc_final: 0.5079 (t0) REVERT: C 315 ILE cc_start: 0.6854 (mm) cc_final: 0.6566 (mt) REVERT: C 578 LYS cc_start: 0.6808 (ptpp) cc_final: 0.5775 (pttt) REVERT: C 579 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7981 (tt) outliers start: 23 outliers final: 16 residues processed: 182 average time/residue: 0.1274 time to fit residues: 35.3962 Evaluate side-chains 178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.194013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118353 restraints weight = 23118.303| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.48 r_work: 0.3072 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18381 Z= 0.143 Angle : 0.621 9.759 25023 Z= 0.303 Chirality : 0.045 0.239 2820 Planarity : 0.005 0.061 3153 Dihedral : 5.325 59.655 2775 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.87 (0.18), residues: 2148 helix: 1.51 (0.21), residues: 648 sheet: -0.52 (0.25), residues: 435 loop : -2.02 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 652 TYR 0.016 0.001 TYR C 707 PHE 0.020 0.001 PHE C 517 TRP 0.008 0.001 TRP A 701 HIS 0.004 0.001 HIS C 624 Details of bonding type rmsd covalent geometry : bond 0.00338 (18336) covalent geometry : angle 0.61609 (24915) SS BOND : bond 0.00232 ( 27) SS BOND : angle 0.98961 ( 54) hydrogen bonds : bond 0.05827 ( 633) hydrogen bonds : angle 4.37887 ( 1737) link_BETA1-4 : bond 0.00420 ( 9) link_BETA1-4 : angle 1.81665 ( 27) link_NAG-ASN : bond 0.00392 ( 9) link_NAG-ASN : angle 1.37419 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.570 Fit side-chains REVERT: A 142 MET cc_start: 0.8405 (mtm) cc_final: 0.8177 (mtp) REVERT: A 248 ASN cc_start: 0.5718 (t0) cc_final: 0.5368 (t0) REVERT: A 309 ASN cc_start: 0.6704 (m110) cc_final: 0.6447 (m-40) REVERT: A 899 GLU cc_start: 0.7774 (tp30) cc_final: 0.7423 (tp30) REVERT: B 230 GLN cc_start: 0.7220 (mt0) cc_final: 0.7014 (mt0) REVERT: B 248 ASN cc_start: 0.5820 (t0) cc_final: 0.5384 (t0) REVERT: B 292 LEU cc_start: 0.1659 (OUTLIER) cc_final: 0.1401 (mm) REVERT: B 309 ASN cc_start: 0.6706 (m110) cc_final: 0.6422 (m-40) REVERT: B 384 GLU cc_start: 0.7577 (mp0) cc_final: 0.7340 (mp0) REVERT: C 248 ASN cc_start: 0.5817 (t0) cc_final: 0.5166 (t0) REVERT: C 292 LEU cc_start: 0.1536 (OUTLIER) cc_final: 0.1216 (mm) REVERT: C 315 ILE cc_start: 0.6903 (mm) cc_final: 0.6576 (mt) REVERT: C 578 LYS cc_start: 0.6769 (ptpp) cc_final: 0.5771 (pttt) REVERT: C 579 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7975 (tt) REVERT: C 751 CYS cc_start: 0.8866 (t) cc_final: 0.8634 (t) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.1351 time to fit residues: 36.4249 Evaluate side-chains 180 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.9631 > 50: distance: 23 - 35: 35.919 distance: 35 - 36: 39.665 distance: 36 - 37: 39.537 distance: 36 - 39: 41.303 distance: 37 - 38: 56.187 distance: 37 - 42: 62.154 distance: 39 - 40: 55.686 distance: 42 - 43: 26.174 distance: 43 - 44: 41.000 distance: 43 - 46: 56.176 distance: 44 - 45: 48.591 distance: 44 - 48: 38.714 distance: 48 - 49: 69.391 distance: 49 - 50: 38.022 distance: 50 - 51: 53.843 distance: 50 - 54: 36.178 distance: 52 - 53: 38.824 distance: 54 - 55: 57.255 distance: 55 - 56: 55.579 distance: 55 - 58: 56.470 distance: 56 - 57: 40.167 distance: 56 - 63: 31.342 distance: 58 - 59: 57.122 distance: 59 - 60: 56.017 distance: 60 - 61: 57.008 distance: 61 - 62: 57.839 distance: 63 - 64: 31.190 distance: 64 - 65: 40.149 distance: 64 - 67: 39.367 distance: 65 - 66: 55.618 distance: 65 - 71: 40.628 distance: 67 - 68: 38.901 distance: 68 - 69: 56.390 distance: 68 - 70: 41.401 distance: 71 - 72: 56.427 distance: 72 - 73: 40.436 distance: 72 - 75: 40.242 distance: 73 - 74: 38.979 distance: 73 - 83: 40.279 distance: 75 - 76: 39.703 distance: 76 - 77: 40.583 distance: 76 - 78: 39.212 distance: 79 - 81: 39.125 distance: 80 - 81: 40.511 distance: 81 - 82: 39.861 distance: 83 - 84: 39.956 distance: 84 - 85: 40.742 distance: 85 - 86: 39.351 distance: 85 - 87: 40.477 distance: 87 - 88: 57.601 distance: 88 - 89: 58.055 distance: 88 - 91: 40.762 distance: 89 - 90: 68.602 distance: 89 - 96: 55.592 distance: 91 - 92: 40.668 distance: 92 - 93: 56.056 distance: 93 - 94: 56.143 distance: 94 - 95: 38.815 distance: 96 - 97: 56.705 distance: 97 - 98: 40.953 distance: 97 - 100: 68.157 distance: 98 - 99: 56.570 distance: 98 - 101: 40.597 distance: 101 - 102: 38.806 distance: 102 - 103: 56.719 distance: 102 - 105: 39.802 distance: 103 - 104: 38.861 distance: 103 - 112: 35.657 distance: 105 - 106: 67.867 distance: 106 - 107: 39.223 distance: 107 - 108: 56.952 distance: 108 - 109: 56.081 distance: 109 - 110: 56.392