Starting phenix.real_space_refine on Wed Sep 17 18:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_30856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_30856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_30856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_30856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtw_30856/09_2025/7dtw_30856.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.72, per 1000 atoms: 0.27 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: 0.99 Conformation dependent library (CDL) restraints added in 601.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 1.55 Time building geometry restraints manager: 1.28 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: 5710 16.63 - 33.26: 438 33.26 - 49.89: 104 49.89 - 66.52: 28 66.52 - 83.15: 10 Dihedral angle restraints: 6290 sinusoidal: 1782 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 6287 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: 1.980 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.610 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 13.830 82.385 3312 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 aren 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 covalent geometry : bond 0.00765 (10424) covalent geometry : angle 1.00780 (14320) SS BOND : bond 0.01549 ( 18) SS BOND : angle 4.22458 ( 36) hydrogen bonds : bond 0.13402 ( 498) hydrogen bonds : angle 6.94805 ( 1422) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 4.64677 ( 12) link_NAG-ASN : bond 0.01081 ( 10) link_NAG-ASN : angle 6.10180 ( 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 : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0825 time to fit residues: 2.3593 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 : 0.194 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=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... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 361 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.038578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.030159 restraints weight = 68605.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030700 restraints weight = 49767.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.031091 restraints weight = 39293.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.031378 restraints weight = 33015.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031571 restraints weight = 29057.145| |-----------------------------------------------------------------------------| r_work (final): 0.2890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.034785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.034762 restraints weight = 783.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.034771 restraints weight = 2.745 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.034766 restraints weight = 738.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.034770 restraints weight = 0.898 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.034766 restraints weight = 570.374| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.030 10456 Z= 0.119 Angle : 0.630 9.236 14398 Z= 0.323 Chirality : 0.047 0.360 1760 Planarity : 0.004 0.033 1904 Dihedral : 8.293 59.606 1904 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.19), residues: 1540 helix: -0.97 (0.18), residues: 658 sheet: -3.62 (0.34), residues: 148 loop : -2.52 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 441 TYR 0.017 0.001 TYR B 421 PHE 0.016 0.001 PHE A 114 TRP 0.008 0.001 TRP B 458 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00231 (10424) covalent geometry : angle 0.58867 (14320) SS BOND : bond 0.00268 ( 18) SS BOND : angle 1.85666 ( 36) hydrogen bonds : bond 0.03881 ( 498) hydrogen bonds : angle 5.68728 ( 1422) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 3.29852 ( 12) link_NAG-ASN : bond 0.01058 ( 10) link_NAG-ASN : angle 4.10046 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 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 : 0.196 Fit side-chains REVERT: B 307 MET cc_start: 0.9088 (mmp) cc_final: 0.8863 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0474 time to fit residues: 1.7058 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 : 0.170 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 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 56 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 overall best weight: 4.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.037240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.029145 restraints weight = 71679.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.029660 restraints weight = 52412.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.030027 restraints weight = 41683.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.030288 restraints weight = 35288.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030422 restraints weight = 31158.116| |-----------------------------------------------------------------------------| r_work (final): 0.2850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.046923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.044619 restraints weight = 321.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.045698 restraints weight = 146.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046449 restraints weight = 80.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.046802 restraints weight = 41.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.046899 restraints weight = 14.953| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10456 Z= 0.207 Angle : 0.634 9.797 14398 Z= 0.335 Chirality : 0.048 0.361 1760 Planarity : 0.003 0.031 1904 Dihedral : 7.742 56.453 1904 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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 aren not related in a simple way. whole: -2.52 (0.20), residues: 1540 helix: -0.46 (0.19), residues: 670 sheet: -3.69 (0.36), residues: 144 loop : -2.42 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 185 TYR 0.019 0.002 TYR A 421 PHE 0.017 0.002 PHE B 522 TRP 0.018 0.002 TRP A 293 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00406 (10424) covalent geometry : angle 0.59655 (14320) SS BOND : bond 0.00738 ( 18) SS BOND : angle 2.09978 ( 36) hydrogen bonds : bond 0.03869 ( 498) hydrogen bonds : angle 5.30584 ( 1422) link_BETA1-4 : bond 0.00483 ( 4) link_BETA1-4 : angle 2.80653 ( 12) link_NAG-ASN : bond 0.00696 ( 10) link_NAG-ASN : angle 3.80143 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.176 Fit side-chains REVERT: B 197 MET cc_start: 0.9500 (mmm) cc_final: 0.9296 (mmm) REVERT: B 307 MET cc_start: 0.9144 (mmp) cc_final: 0.8751 (mmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0445 time to fit residues: 1.1371 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 : 0.200 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 81 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.038195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029847 restraints weight = 68955.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030377 restraints weight = 49930.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030755 restraints weight = 39626.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031031 restraints weight = 33575.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031216 restraints weight = 29616.854| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.048326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.045882 restraints weight = 314.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.046844 restraints weight = 137.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.047786 restraints weight = 77.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048009 restraints weight = 27.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048106 restraints weight = 10.113| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10456 Z= 0.106 Angle : 0.545 9.167 14398 Z= 0.278 Chirality : 0.046 0.358 1760 Planarity : 0.003 0.027 1904 Dihedral : 7.565 59.667 1904 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 aren not related in a simple way. whole: -1.98 (0.22), residues: 1540 helix: 0.07 (0.20), residues: 666 sheet: -3.50 (0.36), residues: 148 loop : -2.18 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 441 TYR 0.017 0.001 TYR A 421 PHE 0.010 0.001 PHE A 68 TRP 0.009 0.001 TRP A 293 HIS 0.002 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00220 (10424) covalent geometry : angle 0.50704 (14320) SS BOND : bond 0.00155 ( 18) SS BOND : angle 1.60590 ( 36) hydrogen bonds : bond 0.03207 ( 498) hydrogen bonds : angle 4.90933 ( 1422) link_BETA1-4 : bond 0.00734 ( 4) link_BETA1-4 : angle 2.80557 ( 12) link_NAG-ASN : bond 0.00741 ( 10) link_NAG-ASN : angle 3.69961 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.209 Fit side-chains REVERT: B 197 MET cc_start: 0.9411 (mmm) cc_final: 0.9086 (mmm) REVERT: B 307 MET cc_start: 0.9108 (mmp) cc_final: 0.8890 (mmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0413 time to fit residues: 1.0664 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 : 0.204 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 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 64 optimal weight: 40.0000 chunk 141 optimal weight: 40.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.029589 restraints weight = 69499.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.030127 restraints weight = 50577.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030507 restraints weight = 40080.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.030769 restraints weight = 33839.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030986 restraints weight = 30019.464| |-----------------------------------------------------------------------------| r_work (final): 0.2872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.049857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047529 restraints weight = 330.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048578 restraints weight = 139.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049467 restraints weight = 77.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.049622 restraints weight = 24.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.049686 restraints weight = 8.586 | |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10456 Z= 0.110 Angle : 0.520 9.134 14398 Z= 0.269 Chirality : 0.045 0.358 1760 Planarity : 0.003 0.024 1904 Dihedral : 7.204 59.151 1904 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 aren not related in a simple way. whole: -1.61 (0.22), residues: 1540 helix: 0.40 (0.20), residues: 672 sheet: -3.38 (0.37), residues: 148 loop : -1.99 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.017 0.001 TYR A 421 PHE 0.008 0.001 PHE B 68 TRP 0.010 0.001 TRP A 293 HIS 0.002 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00220 (10424) covalent geometry : angle 0.48452 (14320) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.37221 ( 36) hydrogen bonds : bond 0.03004 ( 498) hydrogen bonds : angle 4.61778 ( 1422) link_BETA1-4 : bond 0.00546 ( 4) link_BETA1-4 : angle 2.51238 ( 12) link_NAG-ASN : bond 0.00651 ( 10) link_NAG-ASN : angle 3.61453 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 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 : 0.197 Fit side-chains REVERT: B 307 MET cc_start: 0.9076 (mmp) cc_final: 0.8790 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0449 time to fit residues: 1.4829 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 : 0.216 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 2 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 127 optimal weight: 0.0870 chunk 56 optimal weight: 40.0000 chunk 20 optimal weight: 0.0570 chunk 14 optimal weight: 0.0030 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.038422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.030042 restraints weight = 69093.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030569 restraints weight = 50191.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.030957 restraints weight = 39845.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.031247 restraints weight = 33666.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031390 restraints weight = 29548.768| |-----------------------------------------------------------------------------| r_work (final): 0.2889 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.034032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.033800 restraints weight = 614.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.033914 restraints weight = 104.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.033977 restraints weight = 33.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.034017 restraints weight = 12.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.034038 restraints weight = 4.842 | |-----------------------------------------------------------------------------| r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10456 Z= 0.087 Angle : 0.508 8.991 14398 Z= 0.254 Chirality : 0.045 0.350 1760 Planarity : 0.002 0.023 1904 Dihedral : 6.678 55.538 1904 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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 aren not related in a simple way. whole: -1.57 (0.22), residues: 1540 helix: 0.59 (0.20), residues: 678 sheet: -3.87 (0.33), residues: 164 loop : -1.97 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 66 TYR 0.016 0.001 TYR B 421 PHE 0.010 0.001 PHE B 68 TRP 0.007 0.001 TRP A 293 HIS 0.001 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00183 (10424) covalent geometry : angle 0.47090 (14320) SS BOND : bond 0.00109 ( 18) SS BOND : angle 1.30956 ( 36) hydrogen bonds : bond 0.02767 ( 498) hydrogen bonds : angle 4.36147 ( 1422) link_BETA1-4 : bond 0.00633 ( 4) link_BETA1-4 : angle 2.53143 ( 12) link_NAG-ASN : bond 0.00739 ( 10) link_NAG-ASN : angle 3.63308 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.120 Fit side-chains REVERT: B 307 MET cc_start: 0.9145 (mmp) cc_final: 0.8831 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0426 time to fit residues: 1.3130 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 : 0.203 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 : 0.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 78 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 3.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.029448 restraints weight = 70508.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.029947 restraints weight = 51090.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030324 restraints weight = 40855.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030592 restraints weight = 34644.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.030796 restraints weight = 30681.237| |-----------------------------------------------------------------------------| r_work (final): 0.2867 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.051000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.048100 restraints weight = 332.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049244 restraints weight = 152.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050368 restraints weight = 91.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050629 restraints weight = 35.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.050732 restraints weight = 14.409| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10456 Z= 0.143 Angle : 0.531 9.017 14398 Z= 0.275 Chirality : 0.045 0.366 1760 Planarity : 0.003 0.028 1904 Dihedral : 6.799 58.324 1904 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % 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 aren not related in a simple way. whole: -1.47 (0.22), residues: 1540 helix: 0.63 (0.20), residues: 676 sheet: -3.31 (0.35), residues: 162 loop : -2.03 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.016 0.001 TYR B 421 PHE 0.010 0.001 PHE B 522 TRP 0.007 0.001 TRP B 458 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00285 (10424) covalent geometry : angle 0.49613 (14320) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.45974 ( 36) hydrogen bonds : bond 0.02868 ( 498) hydrogen bonds : angle 4.34354 ( 1422) link_BETA1-4 : bond 0.00440 ( 4) link_BETA1-4 : angle 2.39272 ( 12) link_NAG-ASN : bond 0.00596 ( 10) link_NAG-ASN : angle 3.58297 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 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 : 0.196 Fit side-chains REVERT: B 307 MET cc_start: 0.9213 (mmp) cc_final: 0.8862 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0438 time to fit residues: 1.2047 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 : 0.001 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 131 optimal weight: 0.0770 chunk 75 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.029360 restraints weight = 69850.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029884 restraints weight = 50201.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.030270 restraints weight = 39877.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.030547 restraints weight = 33674.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.030756 restraints weight = 29717.331| |-----------------------------------------------------------------------------| r_work (final): 0.2869 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.050015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.047452 restraints weight = 364.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048626 restraints weight = 154.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.049511 restraints weight = 87.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049737 restraints weight = 34.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.049848 restraints weight = 14.719| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10456 Z= 0.119 Angle : 0.510 8.855 14398 Z= 0.260 Chirality : 0.045 0.360 1760 Planarity : 0.003 0.030 1904 Dihedral : 6.715 59.280 1904 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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 aren not related in a simple way. whole: -1.37 (0.22), residues: 1540 helix: 0.72 (0.20), residues: 676 sheet: -3.27 (0.35), residues: 162 loop : -1.97 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 520 TYR 0.015 0.001 TYR B 421 PHE 0.009 0.001 PHE B 522 TRP 0.006 0.001 TRP B 458 HIS 0.003 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00242 (10424) covalent geometry : angle 0.47505 (14320) SS BOND : bond 0.00258 ( 18) SS BOND : angle 1.21324 ( 36) hydrogen bonds : bond 0.02711 ( 498) hydrogen bonds : angle 4.24893 ( 1422) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 2.45997 ( 12) link_NAG-ASN : bond 0.00613 ( 10) link_NAG-ASN : angle 3.57285 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.127 Fit side-chains REVERT: B 197 MET cc_start: 0.9401 (mmm) cc_final: 0.9071 (mmm) REVERT: B 307 MET cc_start: 0.9151 (mmp) cc_final: 0.8798 (mmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0439 time to fit residues: 1.0461 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 : 0.203 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 0.2980 chunk 96 optimal weight: 0.0030 chunk 142 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 115 optimal weight: 4.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.038092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029754 restraints weight = 68364.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.030287 restraints weight = 49339.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030675 restraints weight = 39259.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030943 restraints weight = 33091.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031158 restraints weight = 29229.677| |-----------------------------------------------------------------------------| r_work (final): 0.2884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.050712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047587 restraints weight = 321.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.049387 restraints weight = 148.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049866 restraints weight = 59.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.050084 restraints weight = 27.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.050164 restraints weight = 10.670| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10456 Z= 0.088 Angle : 0.492 8.817 14398 Z= 0.246 Chirality : 0.044 0.353 1760 Planarity : 0.002 0.029 1904 Dihedral : 6.494 58.239 1904 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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 aren not related in a simple way. whole: -1.29 (0.23), residues: 1540 helix: 0.94 (0.20), residues: 670 sheet: -3.49 (0.33), residues: 182 loop : -1.93 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 185 TYR 0.017 0.001 TYR B 421 PHE 0.008 0.001 PHE B 68 TRP 0.008 0.001 TRP B 293 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00181 (10424) covalent geometry : angle 0.45735 (14320) SS BOND : bond 0.00145 ( 18) SS BOND : angle 1.07913 ( 36) hydrogen bonds : bond 0.02475 ( 498) hydrogen bonds : angle 4.04260 ( 1422) link_BETA1-4 : bond 0.00633 ( 4) link_BETA1-4 : angle 2.39438 ( 12) link_NAG-ASN : bond 0.00670 ( 10) link_NAG-ASN : angle 3.56247 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 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 : 0.207 Fit side-chains REVERT: B 197 MET cc_start: 0.9348 (mmm) cc_final: 0.9064 (mmm) REVERT: B 307 MET cc_start: 0.9137 (mmp) cc_final: 0.8786 (mmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0456 time to fit residues: 1.3126 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 : 0.206 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 27 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 87 optimal weight: 40.0000 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.036840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.028727 restraints weight = 71007.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.029240 restraints weight = 51477.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.029615 restraints weight = 40968.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029888 restraints weight = 34620.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.030094 restraints weight = 30590.694| |-----------------------------------------------------------------------------| r_work (final): 0.2846 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.051334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.047570 restraints weight = 306.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.048899 restraints weight = 155.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.050084 restraints weight = 97.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.050478 restraints weight = 46.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050650 restraints weight = 20.557| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10456 Z= 0.198 Angle : 0.576 8.854 14398 Z= 0.303 Chirality : 0.046 0.380 1760 Planarity : 0.003 0.031 1904 Dihedral : 6.606 55.264 1904 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % 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 aren not related in a simple way. whole: -1.48 (0.22), residues: 1540 helix: 0.61 (0.20), residues: 690 sheet: -3.47 (0.33), residues: 176 loop : -1.97 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 520 TYR 0.014 0.001 TYR B 435 PHE 0.015 0.002 PHE B 76 TRP 0.009 0.001 TRP A 70 HIS 0.004 0.002 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00390 (10424) covalent geometry : angle 0.54459 (14320) SS BOND : bond 0.00429 ( 18) SS BOND : angle 1.54780 ( 36) hydrogen bonds : bond 0.02958 ( 498) hydrogen bonds : angle 4.23091 ( 1422) link_BETA1-4 : bond 0.00184 ( 4) link_BETA1-4 : angle 2.21567 ( 12) link_NAG-ASN : bond 0.00597 ( 10) link_NAG-ASN : angle 3.58468 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.258 Fit side-chains REVERT: B 307 MET cc_start: 0.9201 (mmp) cc_final: 0.8793 (mmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0457 time to fit residues: 1.1973 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 : 0.207 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 127 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 138 optimal weight: 0.0040 chunk 53 optimal weight: 40.0000 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.0170 overall best weight: 0.7432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.037938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.029659 restraints weight = 69552.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.030201 restraints weight = 49650.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030598 restraints weight = 39223.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.030892 restraints weight = 32899.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.031091 restraints weight = 28816.564| |-----------------------------------------------------------------------------| r_work (final): 0.2880 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.049864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047139 restraints weight = 331.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048452 restraints weight = 152.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.049117 restraints weight = 75.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049314 restraints weight = 30.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049416 restraints weight = 12.970| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10456 Z= 0.085 Angle : 0.499 8.660 14398 Z= 0.250 Chirality : 0.045 0.366 1760 Planarity : 0.003 0.031 1904 Dihedral : 6.562 59.892 1904 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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 aren not related in a simple way. whole: -1.20 (0.23), residues: 1540 helix: 1.04 (0.20), residues: 670 sheet: -3.79 (0.34), residues: 164 loop : -1.88 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.017 0.001 TYR B 421 PHE 0.008 0.001 PHE B 68 TRP 0.010 0.001 TRP B 293 HIS 0.002 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00174 (10424) covalent geometry : angle 0.46345 (14320) SS BOND : bond 0.00138 ( 18) SS BOND : angle 1.11930 ( 36) hydrogen bonds : bond 0.02462 ( 498) hydrogen bonds : angle 3.98253 ( 1422) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 2.46625 ( 12) link_NAG-ASN : bond 0.00706 ( 10) link_NAG-ASN : angle 3.59755 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.22 seconds wall clock time: 22 minutes 28.24 seconds (1348.24 seconds total)