Starting phenix.real_space_refine on Thu Jul 2 21:30:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2026/7dtw_30856.cif" } resolution = 4.5 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= 0.001 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 44 5.16 5 C 6414 2.51 5 N 1784 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10250 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5027 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1233 Unresolved non-hydrogen angles: 1572 Unresolved non-hydrogen dihedrals: 1050 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'ASP:plan': 15, 'GLN:plan1': 10, 'ARG:plan': 16, 'HIS:plan': 6, 'PHE:plan': 38, 'GLU:plan': 30, 'ASN:plan1': 14, 'TRP:plan': 5, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 686 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5027 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1233 Unresolved non-hydrogen angles: 1572 Unresolved non-hydrogen dihedrals: 1050 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'ASP:plan': 15, 'GLN:plan1': 10, 'ARG:plan': 16, 'HIS:plan': 6, 'PHE:plan': 38, 'GLU:plan': 30, 'ASN:plan1': 14, 'TRP:plan': 5, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 686 Chain: "C" 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 chiralities: 2 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10250 At special positions: 0 Unit cell: (94.34, 102.82, 184.44, 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 44 16.00 O 2008 8.00 N 1784 7.00 C 6414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.07 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.02 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.02 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.02 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.07 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.02 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.02 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.02 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 287 " " NAG A1102 " - " ASN A 446 " " NAG A1103 " - " ASN A 468 " " NAG B1101 " - " ASN B 287 " " NAG B1102 " - " ASN B 446 " " NAG B1103 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 419.1 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 47.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.657A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.242A pdb=" N ASP A 121 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.119A pdb=" N CYS A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.647A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 189 through 205 removed outlier: 4.396A pdb=" N GLN A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.623A pdb=" N LEU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.858A pdb=" N HIS A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.802A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.711A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 removed outlier: 4.044A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 removed outlier: 4.004A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.656A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 697 removed outlier: 4.030A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 746 removed outlier: 4.240A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 796 removed outlier: 3.985A pdb=" N CYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 4.309A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.581A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.658A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.243A pdb=" N ASP B 121 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 4.119A pdb=" N CYS B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.646A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.397A pdb=" N GLN B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.624A pdb=" N LEU B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.858A pdb=" N HIS B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.802A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.711A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.044A pdb=" N SER B 448 " --> pdb=" O THR B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 4.004A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 removed outlier: 3.656A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 697 removed outlier: 4.031A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.239A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 796 removed outlier: 3.985A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 796 " --> pdb=" O PHE B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 4.309A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 858 removed outlier: 3.581A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.527A pdb=" N LYS A 28 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 7.143A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 241 removed outlier: 7.670A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 210 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP A 293 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.638A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 496 removed outlier: 6.357A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.527A pdb=" N LYS B 28 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 removed outlier: 7.143A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 241 removed outlier: 7.671A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 210 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 removed outlier: 3.638A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 496 removed outlier: 6.356A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 550 through 551 498 hydrogen bonds defined for protein. 1422 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: 1.39 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3262 1.33 - 1.46: 2597 1.46 - 1.58: 4513 1.58 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 10424 Sorted by residual: bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CB CYS B 582 " pdb=" SG CYS B 582 " ideal model delta sigma weight residual 1.808 1.746 0.062 3.30e-02 9.18e+02 3.57e+00 ... (remaining 10419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 13746 2.24 - 4.48: 502 4.48 - 6.72: 46 6.72 - 8.96: 18 8.96 - 11.20: 8 Bond angle restraints: 14320 Sorted by residual: angle pdb=" N VAL B 697 " pdb=" CA VAL B 697 " pdb=" C VAL B 697 " ideal model delta sigma weight residual 111.91 108.49 3.42 8.90e-01 1.26e+00 1.47e+01 angle pdb=" N VAL A 697 " pdb=" CA VAL A 697 " pdb=" C VAL A 697 " ideal model delta sigma weight residual 111.91 108.50 3.41 8.90e-01 1.26e+00 1.47e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 113.18 105.17 8.01 2.37e+00 1.78e-01 1.14e+01 angle pdb=" N GLY B 315 " pdb=" CA GLY B 315 " pdb=" C GLY B 315 " ideal model delta sigma weight residual 113.18 105.18 8.00 2.37e+00 1.78e-01 1.14e+01 angle pdb=" C VAL A 313 " pdb=" N VAL A 314 " pdb=" CA VAL A 314 " ideal model delta sigma weight residual 122.50 117.20 5.30 1.60e+00 3.91e-01 1.10e+01 ... (remaining 14315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 5464 16.63 - 33.26: 414 33.26 - 49.89: 84 49.89 - 66.52: 24 66.52 - 83.15: 10 Dihedral angle restraints: 5996 sinusoidal: 1488 harmonic: 4508 Sorted by residual: dihedral pdb=" CB CYS B 568 " pdb=" SG CYS B 568 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 176.15 -83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 176.13 -83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 236 " pdb=" SG CYS B 236 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -26.69 -59.31 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 5993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1550 0.086 - 0.171: 189 0.171 - 0.257: 17 0.257 - 0.342: 2 0.342 - 0.428: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" C1 NAG A1102 " pdb=" ND2 ASN A 446 " pdb=" C2 NAG A1102 " pdb=" O5 NAG A1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 446 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL B 314 " pdb=" CA VAL B 314 " pdb=" CG1 VAL B 314 " pdb=" CG2 VAL B 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1757 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 725 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C PHE B 725 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE B 725 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 726 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 725 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C PHE A 725 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 725 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 726 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 479 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C PHE B 479 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE B 479 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 480 " 0.011 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3114 2.79 - 3.32: 10404 3.32 - 3.85: 18413 3.85 - 4.37: 19836 4.37 - 4.90: 31559 Nonbonded interactions: 83326 Sorted by model distance: nonbonded pdb=" O ALA B 423 " pdb=" OG SER B 426 " model vdw 2.267 3.040 nonbonded pdb=" O ALA A 423 " pdb=" OG SER A 426 " model vdw 2.267 3.040 nonbonded pdb=" O ASN B 400 " pdb=" OG SER B 403 " model vdw 2.281 3.040 nonbonded pdb=" O ASN A 400 " pdb=" OG SER A 403 " model vdw 2.281 3.040 nonbonded pdb=" O GLU A 79 " pdb=" OG SER A 83 " model vdw 2.301 3.040 ... (remaining 83321 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.008 0.062 10456 Z= 0.386 Angle : 1.073 13.769 14398 Z= 0.586 Chirality : 0.058 0.428 1760 Planarity : 0.006 0.041 1904 Dihedral : 13.741 82.385 3018 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -4.26 (0.17), residues: 1540 helix: -2.60 (0.15), residues: 644 sheet: -3.52 (0.35), residues: 122 loop : -2.90 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 185 TYR 0.025 0.003 TYR B 421 PHE 0.028 0.003 PHE A 589 TRP 0.016 0.003 TRP B 293 HIS 0.007 0.003 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.38 (10424) covalent geometry : angle 1.00780 / 0.57 (14320) SS BOND : bond 0.01549 / 1.04 ( 18) SS BOND : angle 4.22458 / 2.71 ( 36) hydrogen bonds : bond 0.13402 / 9.52 ( 498) hydrogen bonds : angle 6.94805 / 4.92 ( 1422) link_BETA1-4 : bond 0.00785 / 0.45 ( 4) link_BETA1-4 : angle 4.64677 / 2.87 ( 12) link_NAG-ASN : bond 0.01081 / 0.70 ( 10) link_NAG-ASN : angle 6.10180 / 4.12 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0601 time to fit residues: 1.7129 Evaluate side-chains 12 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.165 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.038542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030157 restraints weight = 68915.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.030695 restraints weight = 50085.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031067 restraints weight = 39626.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031352 restraints weight = 33460.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.031549 restraints weight = 29479.345| |-----------------------------------------------------------------------------| r_work (final): 0.2887 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.033639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.032065 restraints weight = 782.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.032857 restraints weight = 388.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.033536 restraints weight = 230.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.033614 restraints weight = 48.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.033633 restraints weight = 10.876| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10456 Z= 0.125 Angle : 0.636 9.346 14398 Z= 0.326 Chirality : 0.047 0.369 1760 Planarity : 0.004 0.033 1904 Dihedral : 5.943 26.482 1610 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.94 (0.19), residues: 1540 helix: -0.94 (0.18), residues: 656 sheet: -3.59 (0.34), residues: 148 loop : -2.55 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 441 TYR 0.016 0.001 TYR B 421 PHE 0.012 0.002 PHE A 270 TRP 0.009 0.001 TRP B 458 HIS 0.002 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (10424) covalent geometry : angle 0.59399 / 0.32 (14320) SS BOND : bond 0.00252 / 0.16 ( 18) SS BOND : angle 1.98343 / 1.24 ( 36) hydrogen bonds : bond 0.03952 / 2.66 ( 498) hydrogen bonds : angle 5.66602 / 3.98 ( 1422) link_BETA1-4 : bond 0.00780 / 0.41 ( 4) link_BETA1-4 : angle 3.09606 / 1.70 ( 12) link_NAG-ASN : bond 0.00857 / 0.60 ( 10) link_NAG-ASN : angle 4.14373 / 2.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.248 Fit side-chains REVERT: B 307 MET cc_start: 0.9107 (mmp) cc_final: 0.8871 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0462 time to fit residues: 1.7186 Evaluate side-chains 10 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.182 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 152 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 0.0980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN B 361 GLN B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.038237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029855 restraints weight = 68113.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.030388 restraints weight = 49374.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030768 restraints weight = 39206.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031037 restraints weight = 33079.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031191 restraints weight = 29233.728| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.046441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.043961 restraints weight = 366.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.044986 restraints weight = 152.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.045572 restraints weight = 81.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.045923 restraints weight = 47.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.046134 restraints weight = 28.583| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10456 Z= 0.120 Angle : 0.567 9.476 14398 Z= 0.293 Chirality : 0.046 0.366 1760 Planarity : 0.003 0.031 1904 Dihedral : 5.153 25.661 1610 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.98 (0.21), residues: 1540 helix: 0.10 (0.20), residues: 666 sheet: -3.79 (0.32), residues: 172 loop : -2.04 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.019 0.001 TYR B 421 PHE 0.011 0.001 PHE B 180 TRP 0.022 0.001 TRP B 293 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (10424) covalent geometry : angle 0.52912 / 0.28 (14320) SS BOND : bond 0.00481 / 0.35 ( 18) SS BOND : angle 1.64225 / 1.04 ( 36) hydrogen bonds : bond 0.03460 / 2.34 ( 498) hydrogen bonds : angle 5.08533 / 3.55 ( 1422) link_BETA1-4 : bond 0.00598 / 0.32 ( 4) link_BETA1-4 : angle 2.71217 / 1.45 ( 12) link_NAG-ASN : bond 0.00722 / 0.48 ( 10) link_NAG-ASN : angle 3.81872 / 2.44 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.128 Fit side-chains REVERT: B 197 MET cc_start: 0.9415 (mmm) cc_final: 0.9206 (mmm) REVERT: B 307 MET cc_start: 0.9011 (mmp) cc_final: 0.8711 (mmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0326 time to fit residues: 1.0991 Evaluate side-chains 9 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 7.9990 chunk 96 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.038811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.030144 restraints weight = 69045.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030746 restraints weight = 48058.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031182 restraints weight = 37305.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031491 restraints weight = 30885.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031737 restraints weight = 26943.484| |-----------------------------------------------------------------------------| r_work (final): 0.2887 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.047909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.045204 restraints weight = 467.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.046573 restraints weight = 194.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047194 restraints weight = 94.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047519 restraints weight = 50.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.047687 restraints weight = 26.709| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10456 Z= 0.095 Angle : 0.529 9.135 14398 Z= 0.271 Chirality : 0.045 0.343 1760 Planarity : 0.003 0.027 1904 Dihedral : 4.635 22.717 1610 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.42 (0.22), residues: 1540 helix: 0.60 (0.20), residues: 676 sheet: -3.50 (0.34), residues: 172 loop : -1.80 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.015 0.001 TYR B 421 PHE 0.018 0.001 PHE A 114 TRP 0.007 0.001 TRP A 458 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (10424) covalent geometry : angle 0.49344 / 0.26 (14320) SS BOND : bond 0.00322 / 0.21 ( 18) SS BOND : angle 1.32317 / 0.85 ( 36) hydrogen bonds : bond 0.03149 / 2.10 ( 498) hydrogen bonds : angle 4.72703 / 3.31 ( 1422) link_BETA1-4 : bond 0.00627 / 0.33 ( 4) link_BETA1-4 : angle 2.50893 / 1.33 ( 12) link_NAG-ASN : bond 0.00769 / 0.52 ( 10) link_NAG-ASN : angle 3.65682 / 2.33 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0370 time to fit residues: 1.2915 Evaluate side-chains 11 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.142 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.038747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.030178 restraints weight = 70254.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030735 restraints weight = 51109.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031129 restraints weight = 40361.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.031410 restraints weight = 33898.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.031632 restraints weight = 29976.997| |-----------------------------------------------------------------------------| r_work (final): 0.2889 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.034738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.034572 restraints weight = 691.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.034666 restraints weight = 118.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.034705 restraints weight = 29.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.034726 restraints weight = 8.429 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.034727 restraints weight = 2.259 | |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10456 Z= 0.090 Angle : 0.517 9.082 14398 Z= 0.262 Chirality : 0.045 0.334 1760 Planarity : 0.003 0.023 1904 Dihedral : 4.362 20.694 1610 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.04 (0.23), residues: 1540 helix: 1.01 (0.21), residues: 670 sheet: -3.26 (0.36), residues: 170 loop : -1.72 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 185 TYR 0.016 0.001 TYR B 421 PHE 0.009 0.001 PHE B 68 TRP 0.010 0.001 TRP A 293 HIS 0.002 0.000 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (10424) covalent geometry : angle 0.48378 / 0.25 (14320) SS BOND : bond 0.00172 / 0.12 ( 18) SS BOND : angle 1.16229 / 0.74 ( 36) hydrogen bonds : bond 0.02945 / 1.99 ( 498) hydrogen bonds : angle 4.45087 / 3.12 ( 1422) link_BETA1-4 : bond 0.00499 / 0.27 ( 4) link_BETA1-4 : angle 2.39884 / 1.25 ( 12) link_NAG-ASN : bond 0.00681 / 0.44 ( 10) link_NAG-ASN : angle 3.57559 / 2.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.187 Fit side-chains REVERT: B 307 MET cc_start: 0.8970 (mmp) cc_final: 0.8653 (mmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0286 time to fit residues: 0.8057 Evaluate side-chains 10 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.128 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 112 optimal weight: 0.0980 chunk 140 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 135 optimal weight: 40.0000 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.039361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030649 restraints weight = 68827.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031239 restraints weight = 49121.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.031636 restraints weight = 38546.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.031859 restraints weight = 32397.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.032131 restraints weight = 28942.472| |-----------------------------------------------------------------------------| r_work (final): 0.2910 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.034729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.034564 restraints weight = 672.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.034662 restraints weight = 117.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.034711 restraints weight = 28.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.034723 restraints weight = 8.051 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.034721 restraints weight = 2.263 | |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10456 Z= 0.085 Angle : 0.505 8.895 14398 Z= 0.252 Chirality : 0.046 0.332 1760 Planarity : 0.003 0.025 1904 Dihedral : 4.143 18.609 1610 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.72 (0.23), residues: 1540 helix: 1.31 (0.21), residues: 670 sheet: -3.19 (0.36), residues: 174 loop : -1.54 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.015 0.001 TYR A 421 PHE 0.010 0.001 PHE B 68 TRP 0.006 0.001 TRP A 352 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.08 (10424) covalent geometry : angle 0.47244 / 0.24 (14320) SS BOND : bond 0.00224 / 0.14 ( 18) SS BOND : angle 1.08386 / 0.72 ( 36) hydrogen bonds : bond 0.02726 / 1.83 ( 498) hydrogen bonds : angle 4.23369 / 2.97 ( 1422) link_BETA1-4 : bond 0.00573 / 0.30 ( 4) link_BETA1-4 : angle 2.35089 / 1.25 ( 12) link_NAG-ASN : bond 0.00759 / 0.50 ( 10) link_NAG-ASN : angle 3.48620 / 2.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.120 Fit side-chains REVERT: B 307 MET cc_start: 0.8946 (mmp) cc_final: 0.8557 (mmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0297 time to fit residues: 1.0088 Evaluate side-chains 13 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.122 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 chunk 139 optimal weight: 5.9990 chunk 122 optimal weight: 0.0040 chunk 7 optimal weight: 4.9990 overall best weight: 2.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.038097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029786 restraints weight = 70392.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030306 restraints weight = 51497.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030677 restraints weight = 41025.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.030937 restraints weight = 34863.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.031139 restraints weight = 31044.925| |-----------------------------------------------------------------------------| r_work (final): 0.2874 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.034258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.034100 restraints weight = 671.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.034187 restraints weight = 99.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.034243 restraints weight = 26.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.034257 restraints weight = 8.299 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.034259 restraints weight = 2.656 | |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10456 Z= 0.128 Angle : 0.513 9.040 14398 Z= 0.264 Chirality : 0.044 0.327 1760 Planarity : 0.003 0.028 1904 Dihedral : 4.093 17.773 1610 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.53 (0.23), residues: 1540 helix: 1.54 (0.21), residues: 666 sheet: -3.07 (0.36), residues: 174 loop : -1.51 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 520 TYR 0.015 0.001 TYR B 421 PHE 0.008 0.001 PHE B 114 TRP 0.007 0.001 TRP B 458 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (10424) covalent geometry : angle 0.48104 / 0.26 (14320) SS BOND : bond 0.00306 / 0.20 ( 18) SS BOND : angle 1.17642 / 0.76 ( 36) hydrogen bonds : bond 0.02802 / 1.90 ( 498) hydrogen bonds : angle 4.22475 / 2.95 ( 1422) link_BETA1-4 : bond 0.00312 / 0.17 ( 4) link_BETA1-4 : angle 2.22803 / 1.13 ( 12) link_NAG-ASN : bond 0.00600 / 0.38 ( 10) link_NAG-ASN : angle 3.49810 / 2.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.141 Fit side-chains REVERT: B 307 MET cc_start: 0.9159 (mmp) cc_final: 0.8849 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0393 time to fit residues: 1.0281 Evaluate side-chains 10 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.111 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 8.9990 chunk 139 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 47 optimal weight: 0.0270 chunk 53 optimal weight: 0.0030 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 1.0250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.030189 restraints weight = 69092.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030737 restraints weight = 50080.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031105 restraints weight = 39891.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031389 restraints weight = 33956.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031584 restraints weight = 29869.592| |-----------------------------------------------------------------------------| r_work (final): 0.2896 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.049646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047599 restraints weight = 410.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048513 restraints weight = 160.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.049044 restraints weight = 82.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 8)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049308 restraints weight = 44.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049441 restraints weight = 24.060| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10456 Z= 0.082 Angle : 0.489 8.798 14398 Z= 0.244 Chirality : 0.044 0.330 1760 Planarity : 0.002 0.027 1904 Dihedral : 3.969 16.329 1610 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.39 (0.23), residues: 1540 helix: 1.64 (0.21), residues: 670 sheet: -2.94 (0.37), residues: 172 loop : -1.45 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.014 0.001 TYR B 421 PHE 0.008 0.001 PHE B 68 TRP 0.006 0.001 TRP B 293 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.08 (10424) covalent geometry : angle 0.45693 / 0.24 (14320) SS BOND : bond 0.00137 / 0.09 ( 18) SS BOND : angle 0.99664 / 0.66 ( 36) hydrogen bonds : bond 0.02564 / 1.73 ( 498) hydrogen bonds : angle 4.06278 / 2.85 ( 1422) link_BETA1-4 : bond 0.00575 / 0.31 ( 4) link_BETA1-4 : angle 2.26808 / 1.19 ( 12) link_NAG-ASN : bond 0.00696 / 0.46 ( 10) link_NAG-ASN : angle 3.43464 / 2.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.144 Fit side-chains REVERT: B 197 MET cc_start: 0.9401 (mmm) cc_final: 0.9168 (mmm) REVERT: B 307 MET cc_start: 0.9062 (mmp) cc_final: 0.8750 (mmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0289 time to fit residues: 0.8121 Evaluate side-chains 12 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 127 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 89 optimal weight: 0.0030 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 88 optimal weight: 0.0670 chunk 86 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 0.0870 chunk 119 optimal weight: 8.9990 overall best weight: 2.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.029597 restraints weight = 69859.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030130 restraints weight = 51283.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030509 restraints weight = 40953.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.030784 restraints weight = 34796.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.030915 restraints weight = 30801.414| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.034690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.034522 restraints weight = 569.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.034626 restraints weight = 86.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.034666 restraints weight = 23.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.034684 restraints weight = 7.567 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.034685 restraints weight = 2.538 | |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10456 Z= 0.121 Angle : 0.504 8.835 14398 Z= 0.258 Chirality : 0.044 0.340 1760 Planarity : 0.003 0.028 1904 Dihedral : 3.984 15.665 1610 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.37 (0.23), residues: 1540 helix: 1.72 (0.21), residues: 670 sheet: -3.02 (0.37), residues: 172 loop : -1.49 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.014 0.001 TYR B 421 PHE 0.011 0.001 PHE B 38 TRP 0.005 0.001 TRP A 458 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10424) covalent geometry : angle 0.47236 / 0.25 (14320) SS BOND : bond 0.00280 / 0.18 ( 18) SS BOND : angle 1.14034 / 0.74 ( 36) hydrogen bonds : bond 0.02607 / 1.77 ( 498) hydrogen bonds : angle 3.99703 / 2.80 ( 1422) link_BETA1-4 : bond 0.00292 / 0.16 ( 4) link_BETA1-4 : angle 2.16878 / 1.09 ( 12) link_NAG-ASN : bond 0.00608 / 0.38 ( 10) link_NAG-ASN : angle 3.43131 / 2.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.111 Fit side-chains REVERT: B 197 MET cc_start: 0.9412 (mmm) cc_final: 0.9161 (mmm) REVERT: B 307 MET cc_start: 0.9180 (mmp) cc_final: 0.8735 (mmm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0366 time to fit residues: 0.8467 Evaluate side-chains 10 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.178 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 overall best weight: 1.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.038558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.029945 restraints weight = 68954.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030532 restraints weight = 48399.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.030953 restraints weight = 37944.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.031246 restraints weight = 31808.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.031409 restraints weight = 27986.438| |-----------------------------------------------------------------------------| r_work (final): 0.2889 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046558 restraints weight = 348.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.047743 restraints weight = 167.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.048557 restraints weight = 94.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.048804 restraints weight = 42.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.048906 restraints weight = 20.050| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10456 Z= 0.081 Angle : 0.482 8.713 14398 Z= 0.241 Chirality : 0.044 0.331 1760 Planarity : 0.003 0.030 1904 Dihedral : 3.828 15.540 1610 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.21 (0.24), residues: 1540 helix: 1.75 (0.21), residues: 680 sheet: -2.89 (0.38), residues: 172 loop : -1.36 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.016 0.001 TYR A 421 PHE 0.007 0.001 PHE B 68 TRP 0.007 0.001 TRP B 293 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.08 (10424) covalent geometry : angle 0.45060 / 0.23 (14320) SS BOND : bond 0.00141 / 0.09 ( 18) SS BOND : angle 0.94309 / 0.62 ( 36) hydrogen bonds : bond 0.02398 / 1.62 ( 498) hydrogen bonds : angle 3.88328 / 2.72 ( 1422) link_BETA1-4 : bond 0.00627 / 0.33 ( 4) link_BETA1-4 : angle 2.21610 / 1.15 ( 12) link_NAG-ASN : bond 0.00672 / 0.44 ( 10) link_NAG-ASN : angle 3.41798 / 2.19 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.114 Fit side-chains REVERT: B 197 MET cc_start: 0.9331 (mmm) cc_final: 0.9090 (mmm) REVERT: B 307 MET cc_start: 0.8969 (mmp) cc_final: 0.8577 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0359 time to fit residues: 0.9259 Evaluate side-chains 12 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.120 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 148 optimal weight: 0.0030 chunk 74 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.037708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.029383 restraints weight = 69793.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.029915 restraints weight = 50471.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030275 restraints weight = 40033.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030560 restraints weight = 34075.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.030777 restraints weight = 29968.641| |-----------------------------------------------------------------------------| r_work (final): 0.2872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.035824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.035734 restraints weight = 465.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.035788 restraints weight = 43.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.035826 restraints weight = 13.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.035824 restraints weight = 4.213 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.035822 restraints weight = 1.344 | |-----------------------------------------------------------------------------| r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10456 Z= 0.128 Angle : 0.508 8.782 14398 Z= 0.262 Chirality : 0.044 0.338 1760 Planarity : 0.003 0.031 1904 Dihedral : 3.932 15.139 1610 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1540 helix: 1.75 (0.21), residues: 680 sheet: -3.02 (0.36), residues: 176 loop : -1.34 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.013 0.001 TYR B 421 PHE 0.012 0.001 PHE B 76 TRP 0.006 0.001 TRP A 70 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (10424) covalent geometry : angle 0.47689 / 0.25 (14320) SS BOND : bond 0.00358 / 0.23 ( 18) SS BOND : angle 1.15334 / 0.75 ( 36) hydrogen bonds : bond 0.02553 / 1.74 ( 498) hydrogen bonds : angle 3.86943 / 2.70 ( 1422) link_BETA1-4 : bond 0.00317 / 0.17 ( 4) link_BETA1-4 : angle 2.11904 / 1.05 ( 12) link_NAG-ASN : bond 0.00603 / 0.38 ( 10) link_NAG-ASN : angle 3.41515 / 2.20 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.92 seconds wall clock time: 18 minutes 27.07 seconds (1107.07 seconds total)