Starting phenix.real_space_refine on Wed Jan 22 05:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm1_19348/01_2025/8rm1_19348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm1_19348/01_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_19348/01_2025/8rm1_19348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm1_19348/01_2025/8rm1_19348.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm1_19348/01_2025/8rm1_19348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm1_19348/01_2025/8rm1_19348.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2} 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: C, B, F, H, G, I Time building chain proxies: 13.67, per 1000 atoms: 0.76 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=9, 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 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: 5.02 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.86 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: 6.09 Time building geometry restraints manager: 5.77 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: 10586 21.88 - 43.75: 602 43.75 - 65.63: 101 65.63 - 87.51: 39 87.51 - 109.38: 12 Dihedral angle restraints: 11340 sinusoidal: 4851 harmonic: 6489 Sorted by residual: 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 A 256 " pdb=" SG CYS A 256 " pdb=" SG CYS A 380 " pdb=" CB CYS A 380 " ideal model delta sinusoidal sigma weight residual 93.00 177.14 -84.14 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A 417 " pdb=" SG CYS A 417 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 162.09 -69.09 1 1.00e+01 1.00e-02 6.17e+01 ... (remaining 11337 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: 2.03 - 2.60: 129 2.60 - 3.18: 14567 3.18 - 3.75: 25274 3.75 - 4.33: 34822 4.33 - 4.90: 58650 Nonbonded interactions: 133442 Sorted by model distance: nonbonded pdb=" SG CYS C 779 " pdb=" SG CYS C 788 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 779 " pdb=" SG CYS B 788 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 446 " pdb=" SG CYS B 454 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 446 " pdb=" SG CYS C 454 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 235 " pdb=" SG CYS B 318 " model vdw 2.031 3.760 ... (remaining 133437 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 44.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- 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 18336 Z= 0.202 Angle : 0.659 9.740 24915 Z= 0.336 Chirality : 0.044 0.281 2820 Planarity : 0.005 0.085 3153 Dihedral : 14.776 109.384 7125 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (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 TRP 0.009 0.001 TRP C 720 HIS 0.003 0.001 HIS B 624 PHE 0.008 0.001 PHE C 838 TYR 0.011 0.001 TYR C 688 ARG 0.003 0.000 ARG A 652 *********************** 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 : 2.170 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: 0.2876 time to fit residues: 97.0988 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 : 1.946 ------------------------------------------------------------------------------- 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 182 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 591 GLN A 595 GLN B 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.192256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115927 restraints weight = 23301.232| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.47 r_work: 0.2955 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18336 Z= 0.338 Angle : 0.690 12.112 24915 Z= 0.346 Chirality : 0.049 0.263 2820 Planarity : 0.005 0.069 3153 Dihedral : 8.088 61.829 2784 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.36 % Allowed : 5.00 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2148 helix: 1.38 (0.21), residues: 648 sheet: -0.16 (0.26), residues: 411 loop : -1.86 (0.16), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 720 HIS 0.005 0.001 HIS C 624 PHE 0.020 0.002 PHE C 517 TYR 0.022 0.002 TYR B 707 ARG 0.002 0.000 ARG C 763 *********************** 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 : 1.951 Fit side-chains REVERT: A 198 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 230 GLN cc_start: 0.7334 (mt0) cc_final: 0.7046 (mt0) REVERT: A 248 ASN cc_start: 0.5759 (t0) cc_final: 0.5383 (t0) REVERT: A 384 GLU cc_start: 0.7357 (mp0) cc_final: 0.7122 (mp0) REVERT: A 899 GLU cc_start: 0.8005 (tp30) cc_final: 0.7559 (tp30) REVERT: B 198 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: B 248 ASN cc_start: 0.5600 (t0) cc_final: 0.4965 (t0) REVERT: B 298 MET cc_start: 0.5901 (tpt) cc_final: 0.5660 (tpt) REVERT: B 384 GLU cc_start: 0.7282 (mp0) cc_final: 0.7052 (mp0) REVERT: C 198 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: C 248 ASN cc_start: 0.5748 (t0) cc_final: 0.5200 (t0) REVERT: C 315 ILE cc_start: 0.6629 (mm) cc_final: 0.6400 (mt) outliers start: 27 outliers final: 17 residues processed: 198 average time/residue: 0.3103 time to fit residues: 93.5793 Evaluate side-chains 190 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 2.340 ------------------------------------------------------------------------------- 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 367 LEU Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 LEU 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 6 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN B 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.193815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118805 restraints weight = 23248.951| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.45 r_work: 0.2968 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18336 Z= 0.256 Angle : 0.616 11.777 24915 Z= 0.307 Chirality : 0.046 0.239 2820 Planarity : 0.005 0.061 3153 Dihedral : 6.573 58.822 2784 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.57 % Allowed : 7.68 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2148 helix: 1.29 (0.21), residues: 669 sheet: -0.22 (0.26), residues: 411 loop : -1.98 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.004 0.001 HIS C 624 PHE 0.020 0.002 PHE C 517 TYR 0.016 0.001 TYR B 707 ARG 0.002 0.000 ARG B 436 *********************** 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 208 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.934 Fit side-chains REVERT: A 230 GLN cc_start: 0.7334 (mt0) cc_final: 0.6874 (mt0) REVERT: A 248 ASN cc_start: 0.5621 (t0) cc_final: 0.5222 (t0) REVERT: A 384 GLU cc_start: 0.7375 (mp0) cc_final: 0.7106 (mp0) REVERT: B 230 GLN cc_start: 0.7180 (mt0) cc_final: 0.6973 (mt0) REVERT: B 248 ASN cc_start: 0.5518 (t0) cc_final: 0.5064 (t0) REVERT: B 384 GLU cc_start: 0.7328 (mp0) cc_final: 0.6972 (mp0) REVERT: C 140 VAL cc_start: 0.7652 (m) cc_final: 0.7403 (t) REVERT: C 198 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: C 248 ASN cc_start: 0.5711 (t0) cc_final: 0.5136 (t0) REVERT: C 315 ILE cc_start: 0.6725 (mm) cc_final: 0.6495 (mt) REVERT: C 817 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7236 (p) outliers start: 31 outliers final: 14 residues processed: 199 average time/residue: 0.2784 time to fit residues: 87.1166 Evaluate side-chains 184 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 B residue 147 GLN Chi-restraints excluded: chain B residue 161 THR 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 147 GLN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 817 THR 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 140 optimal weight: 0.0030 chunk 112 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 210 optimal weight: 0.0270 overall best weight: 0.3648 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.198055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123843 restraints weight = 23431.254| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.41 r_work: 0.3074 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18336 Z= 0.129 Angle : 0.555 13.134 24915 Z= 0.268 Chirality : 0.043 0.242 2820 Planarity : 0.004 0.045 3153 Dihedral : 5.521 57.606 2778 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.01 % Allowed : 9.65 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2148 helix: 1.76 (0.22), residues: 645 sheet: -0.20 (0.25), residues: 429 loop : -1.81 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 720 HIS 0.003 0.001 HIS C 867 PHE 0.020 0.001 PHE C 517 TYR 0.014 0.001 TYR C 688 ARG 0.001 0.000 ARG A 226 *********************** 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 193 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 2.151 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.7128 (mt0) cc_final: 0.6914 (mt0) REVERT: A 248 ASN cc_start: 0.5434 (t0) cc_final: 0.4996 (t0) REVERT: A 384 GLU cc_start: 0.7259 (mp0) cc_final: 0.6978 (mp0) REVERT: B 140 VAL cc_start: 0.7390 (m) cc_final: 0.7189 (t) REVERT: B 230 GLN cc_start: 0.7102 (mt0) cc_final: 0.6878 (mt0) REVERT: B 248 ASN cc_start: 0.5458 (t0) cc_final: 0.4980 (t0) REVERT: B 384 GLU cc_start: 0.7221 (mp0) cc_final: 0.6995 (mp0) REVERT: C 248 ASN cc_start: 0.5513 (t0) cc_final: 0.5099 (t0) REVERT: C 315 ILE cc_start: 0.6641 (mm) cc_final: 0.6328 (mt) REVERT: C 817 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7104 (m) outliers start: 20 outliers final: 9 residues processed: 186 average time/residue: 0.2970 time to fit residues: 86.9199 Evaluate side-chains 175 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 LEU Chi-restraints excluded: chain B residue 740 LEU 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 817 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.193867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121648 restraints weight = 23523.144| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.38 r_work: 0.2999 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18336 Z= 0.192 Angle : 0.573 12.444 24915 Z= 0.281 Chirality : 0.044 0.239 2820 Planarity : 0.004 0.051 3153 Dihedral : 5.589 58.939 2778 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.36 % Allowed : 10.81 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2148 helix: 1.73 (0.22), residues: 648 sheet: -0.26 (0.25), residues: 429 loop : -1.82 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 720 HIS 0.004 0.001 HIS C 624 PHE 0.016 0.001 PHE C 517 TYR 0.015 0.001 TYR B 707 ARG 0.001 0.000 ARG B 283 *********************** 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 190 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 2.188 Fit side-chains REVERT: A 140 VAL cc_start: 0.7361 (m) cc_final: 0.7144 (t) REVERT: A 248 ASN cc_start: 0.5521 (t0) cc_final: 0.5126 (t0) REVERT: B 230 GLN cc_start: 0.7157 (mt0) cc_final: 0.6940 (mt0) REVERT: B 248 ASN cc_start: 0.5581 (t0) cc_final: 0.5135 (t0) REVERT: B 384 GLU cc_start: 0.7434 (mp0) cc_final: 0.7168 (mp0) REVERT: B 579 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 248 ASN cc_start: 0.5587 (t0) cc_final: 0.5003 (t0) REVERT: C 315 ILE cc_start: 0.6715 (mm) cc_final: 0.6386 (mt) REVERT: C 578 LYS cc_start: 0.6705 (ptpp) cc_final: 0.5612 (pttt) REVERT: C 579 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7927 (tt) REVERT: C 817 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7222 (m) outliers start: 27 outliers final: 13 residues processed: 180 average time/residue: 0.3029 time to fit residues: 84.6724 Evaluate side-chains 175 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 740 LEU 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 579 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain C residue 198 GLU 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 817 THR 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 191 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 102 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.194223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118463 restraints weight = 23542.777| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.17 r_work: 0.3027 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18336 Z= 0.175 Angle : 0.563 10.277 24915 Z= 0.276 Chirality : 0.044 0.238 2820 Planarity : 0.004 0.048 3153 Dihedral : 5.587 59.188 2778 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.97 % Allowed : 10.56 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2148 helix: 1.75 (0.22), residues: 648 sheet: -0.24 (0.25), residues: 429 loop : -1.82 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 701 HIS 0.003 0.001 HIS C 624 PHE 0.015 0.001 PHE C 517 TYR 0.014 0.001 TYR A 707 ARG 0.001 0.000 ARG B 283 *********************** 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 206 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 2.006 Fit side-chains REVERT: A 230 GLN cc_start: 0.7247 (mt0) cc_final: 0.6996 (mt0) REVERT: A 248 ASN cc_start: 0.5615 (t0) cc_final: 0.5241 (t0) REVERT: B 230 GLN cc_start: 0.7134 (mt0) cc_final: 0.6921 (mt0) REVERT: B 248 ASN cc_start: 0.5597 (t0) cc_final: 0.5150 (t0) REVERT: B 384 GLU cc_start: 0.7441 (mp0) cc_final: 0.7136 (mp0) REVERT: C 248 ASN cc_start: 0.5635 (t0) cc_final: 0.5046 (t0) REVERT: C 315 ILE cc_start: 0.6678 (mm) cc_final: 0.6339 (mt) REVERT: C 579 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8073 (tt) outliers start: 39 outliers final: 22 residues processed: 194 average time/residue: 0.2882 time to fit residues: 87.8529 Evaluate side-chains 185 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 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 622 THR 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 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 619 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 13 optimal weight: 0.0000 chunk 76 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.193970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118265 restraints weight = 23373.027| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.07 r_work: 0.3039 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18336 Z= 0.173 Angle : 0.565 10.058 24915 Z= 0.275 Chirality : 0.044 0.240 2820 Planarity : 0.004 0.048 3153 Dihedral : 5.468 59.597 2775 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.46 % Allowed : 11.21 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2148 helix: 1.78 (0.22), residues: 648 sheet: -0.23 (0.25), residues: 429 loop : -1.82 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 701 HIS 0.003 0.001 HIS A 867 PHE 0.020 0.001 PHE A 517 TYR 0.014 0.001 TYR B 707 ARG 0.002 0.000 ARG A 226 *********************** 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 193 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.017 Fit side-chains REVERT: A 142 MET cc_start: 0.8323 (mtt) cc_final: 0.8059 (mtt) REVERT: A 230 GLN cc_start: 0.7212 (mt0) cc_final: 0.6924 (mt0) REVERT: A 248 ASN cc_start: 0.5626 (t0) cc_final: 0.5257 (t0) REVERT: B 230 GLN cc_start: 0.7108 (mt0) cc_final: 0.6894 (mt0) REVERT: B 248 ASN cc_start: 0.5578 (t0) cc_final: 0.5142 (t0) REVERT: B 292 LEU cc_start: 0.1642 (OUTLIER) cc_final: 0.1380 (mm) REVERT: B 384 GLU cc_start: 0.7470 (mp0) cc_final: 0.7200 (mp0) REVERT: C 248 ASN cc_start: 0.5645 (t0) cc_final: 0.5052 (t0) REVERT: C 292 LEU cc_start: 0.1703 (OUTLIER) cc_final: 0.1391 (mm) REVERT: C 315 ILE cc_start: 0.6717 (mm) cc_final: 0.6438 (mt) REVERT: C 579 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7977 (tt) outliers start: 29 outliers final: 25 residues processed: 185 average time/residue: 0.2949 time to fit residues: 84.4171 Evaluate side-chains 189 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 626 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 367 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 765 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 626 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.193232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117771 restraints weight = 23415.234| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.52 r_work: 0.2982 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18336 Z= 0.197 Angle : 0.577 10.172 24915 Z= 0.282 Chirality : 0.044 0.238 2820 Planarity : 0.004 0.050 3153 Dihedral : 5.373 58.746 2775 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.72 % Allowed : 11.01 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2148 helix: 1.65 (0.21), residues: 669 sheet: -0.24 (0.25), residues: 429 loop : -1.86 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 701 HIS 0.004 0.001 HIS C 624 PHE 0.021 0.001 PHE C 517 TYR 0.015 0.001 TYR C 707 ARG 0.002 0.000 ARG A 283 *********************** 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 199 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 2.109 Fit side-chains REVERT: A 230 GLN cc_start: 0.7190 (mt0) cc_final: 0.6906 (mt0) REVERT: A 248 ASN cc_start: 0.5618 (t0) cc_final: 0.5248 (t0) REVERT: A 292 LEU cc_start: 0.1620 (OUTLIER) cc_final: 0.1213 (mm) REVERT: B 230 GLN cc_start: 0.7149 (mt0) cc_final: 0.6932 (mt0) REVERT: B 248 ASN cc_start: 0.5677 (t0) cc_final: 0.5245 (t0) REVERT: B 292 LEU cc_start: 0.1617 (OUTLIER) cc_final: 0.1353 (mm) REVERT: B 384 GLU cc_start: 0.7472 (mp0) cc_final: 0.7193 (mp0) REVERT: C 248 ASN cc_start: 0.5620 (t0) cc_final: 0.5010 (t0) REVERT: C 292 LEU cc_start: 0.1580 (OUTLIER) cc_final: 0.1259 (mm) REVERT: C 315 ILE cc_start: 0.6725 (mm) cc_final: 0.6459 (mt) REVERT: C 578 LYS cc_start: 0.6668 (ptpp) cc_final: 0.5648 (pttt) REVERT: C 579 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7943 (tt) outliers start: 34 outliers final: 29 residues processed: 190 average time/residue: 0.2915 time to fit residues: 85.9571 Evaluate side-chains 195 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 2.006 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 869 VAL 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 319 SER Chi-restraints excluded: chain B residue 367 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 765 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 619 MET 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 840 VAL 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 41 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 151 optimal weight: 0.0030 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.194555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119253 restraints weight = 23504.576| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.06 r_work: 0.3058 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18336 Z= 0.148 Angle : 0.546 9.844 24915 Z= 0.265 Chirality : 0.043 0.236 2820 Planarity : 0.004 0.047 3153 Dihedral : 5.011 57.387 2775 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2148 helix: 1.78 (0.21), residues: 666 sheet: -0.19 (0.25), residues: 429 loop : -1.83 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 701 HIS 0.003 0.001 HIS C 867 PHE 0.021 0.001 PHE C 517 TYR 0.013 0.001 TYR A 707 ARG 0.001 0.000 ARG A 283 *********************** 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 196 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 2.062 Fit side-chains REVERT: A 248 ASN cc_start: 0.5578 (t0) cc_final: 0.5163 (t0) REVERT: A 292 LEU cc_start: 0.1537 (OUTLIER) cc_final: 0.1243 (mm) REVERT: B 226 ARG cc_start: 0.6768 (ttm170) cc_final: 0.5571 (tpp-160) REVERT: B 248 ASN cc_start: 0.5738 (t0) cc_final: 0.5288 (t0) REVERT: B 292 LEU cc_start: 0.1569 (OUTLIER) cc_final: 0.1311 (mm) REVERT: B 384 GLU cc_start: 0.7452 (mp0) cc_final: 0.7194 (mp0) REVERT: C 248 ASN cc_start: 0.5631 (t0) cc_final: 0.5005 (t0) REVERT: C 292 LEU cc_start: 0.1502 (OUTLIER) cc_final: 0.1183 (mm) REVERT: C 578 LYS cc_start: 0.6664 (ptpp) cc_final: 0.5629 (pttt) REVERT: C 579 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7962 (tt) outliers start: 34 outliers final: 26 residues processed: 185 average time/residue: 0.2842 time to fit residues: 83.2336 Evaluate side-chains 191 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 869 VAL 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 319 SER Chi-restraints excluded: chain B residue 367 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 765 LEU Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 626 ILE 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 773 VAL Chi-restraints excluded: chain C residue 840 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 0.1980 chunk 148 optimal weight: 0.0970 chunk 201 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.196635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121652 restraints weight = 23294.720| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.07 r_work: 0.3088 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18336 Z= 0.127 Angle : 0.532 9.579 24915 Z= 0.256 Chirality : 0.043 0.234 2820 Planarity : 0.004 0.047 3153 Dihedral : 4.676 57.155 2775 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.41 % Allowed : 11.57 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 2148 helix: 1.85 (0.21), residues: 669 sheet: -0.14 (0.26), residues: 429 loop : -1.77 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 701 HIS 0.003 0.000 HIS C 867 PHE 0.021 0.001 PHE A 517 TYR 0.013 0.001 TYR C 688 ARG 0.003 0.000 ARG A 226 ********************** REFINEMENT MACRO_CYCLE 10 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: 28 poor density : 170 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.5663 (t0) cc_final: 0.5007 (t0) REVERT: B 226 ARG cc_start: 0.6812 (ttm170) cc_final: 0.5606 (tpp-160) REVERT: B 248 ASN cc_start: 0.5668 (t0) cc_final: 0.5223 (t0) REVERT: B 292 LEU cc_start: 0.1573 (OUTLIER) cc_final: 0.1325 (mm) REVERT: B 315 ILE cc_start: 0.6544 (mm) cc_final: 0.6276 (mt) REVERT: B 384 GLU cc_start: 0.7467 (mp0) cc_final: 0.7219 (mp0) REVERT: C 248 ASN cc_start: 0.5606 (t0) cc_final: 0.4982 (t0) REVERT: C 292 LEU cc_start: 0.1491 (OUTLIER) cc_final: 0.1175 (mm) REVERT: C 388 LEU cc_start: 0.6317 (mp) cc_final: 0.5914 (tp) REVERT: C 579 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7970 (tt) outliers start: 28 outliers final: 21 residues processed: 189 average time/residue: 0.2812 time to fit residues: 83.7393 Evaluate side-chains 190 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 869 VAL 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 367 LEU Chi-restraints excluded: chain B residue 584 TYR 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 765 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 626 ILE 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 840 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 49 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 81 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 = 0.195036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123033 restraints weight = 23364.281| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.43 r_work: 0.3011 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18336 Z= 0.159 Angle : 0.543 9.773 24915 Z= 0.264 Chirality : 0.043 0.235 2820 Planarity : 0.004 0.048 3153 Dihedral : 4.710 58.098 2775 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.36 % Allowed : 11.72 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 2148 helix: 1.83 (0.21), residues: 669 sheet: -0.15 (0.26), residues: 429 loop : -1.77 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 701 HIS 0.003 0.001 HIS A 867 PHE 0.020 0.001 PHE A 517 TYR 0.014 0.001 TYR B 707 ARG 0.001 0.000 ARG B 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13769.24 seconds wall clock time: 243 minutes 41.99 seconds (14621.99 seconds total)