Starting phenix.real_space_refine on Mon Jul 28 13:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtw_30856/07_2025/7dtw_30856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtw_30856/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2025/7dtw_30856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2025/7dtw_30856.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2025/7dtw_30856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtw_30856/07_2025/7dtw_30856.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 10, 'ASP:plan': 15, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 5, 'HIS:plan': 6, 'PHE:plan': 38, 'GLU:plan': 30, 'ARG:plan': 16} 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: {'GLN:plan1': 10, 'ASP:plan': 15, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 5, 'HIS:plan': 6, 'PHE:plan': 38, 'GLU:plan': 30, 'ARG:plan': 16} 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: 7.21, per 1000 atoms: 0.70 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.36 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: 3.74 Time building geometry restraints manager: 3.35 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: 0.00 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: 4.030 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.530 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- 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 : 9.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP B 293 HIS 0.007 0.003 HIS A 312 PHE 0.028 0.003 PHE A 589 TYR 0.025 0.003 TYR B 421 ARG 0.007 0.001 ARG A 185 Details of bonding type rmsd link_NAG-ASN : bond 0.01081 ( 10) link_NAG-ASN : angle 6.10180 ( 30) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 4.64677 ( 12) hydrogen bonds : bond 0.13402 ( 498) hydrogen bonds : angle 6.94805 ( 1422) SS BOND : bond 0.01549 ( 18) SS BOND : angle 4.22458 ( 36) covalent geometry : bond 0.00765 (10424) covalent geometry : angle 1.00780 (14320) *********************** 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 : 0.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1743 time to fit residues: 5.2451 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 : 0.564 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: 0.0023 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 130 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 40.0000 chunk 39 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.037779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.029552 restraints weight = 69602.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.030071 restraints weight = 50207.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.030453 restraints weight = 39744.589| |-----------------------------------------------------------------------------| r_work (final): 0.2849 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.034648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.034618 restraints weight = 709.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.034644 restraints weight = 28.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.034637 restraints weight = 2.640 | |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10456 Z= 0.158 Angle : 0.660 9.671 14398 Z= 0.345 Chirality : 0.047 0.379 1760 Planarity : 0.004 0.035 1904 Dihedral : 8.367 58.222 1904 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.19), residues: 1540 helix: -0.98 (0.18), residues: 660 sheet: -3.64 (0.34), residues: 142 loop : -2.58 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.003 0.001 HIS A 338 PHE 0.016 0.002 PHE B 522 TYR 0.018 0.001 TYR A 421 ARG 0.003 0.001 ARG B 69 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 10) link_NAG-ASN : angle 4.08646 ( 30) link_BETA1-4 : bond 0.00106 ( 4) link_BETA1-4 : angle 3.34492 ( 12) hydrogen bonds : bond 0.04153 ( 498) hydrogen bonds : angle 5.76730 ( 1422) SS BOND : bond 0.00267 ( 18) SS BOND : angle 2.06581 ( 36) covalent geometry : bond 0.00310 (10424) covalent geometry : angle 0.61875 (14320) *********************** 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 19 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.580 Fit side-chains REVERT: B 197 MET cc_start: 0.9456 (mmm) cc_final: 0.9212 (mmm) REVERT: B 307 MET cc_start: 0.9113 (mmp) cc_final: 0.8818 (mmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1232 time to fit residues: 4.1180 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 : 0.547 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 148 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.0966 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.038455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.029995 restraints weight = 67555.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.030535 restraints weight = 49704.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030925 restraints weight = 39147.245| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.046155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.043530 restraints weight = 359.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.044535 restraints weight = 163.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.045335 restraints weight = 93.222| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2287 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= 0.105 Angle : 0.558 9.443 14398 Z= 0.284 Chirality : 0.046 0.365 1760 Planarity : 0.003 0.029 1904 Dihedral : 7.606 58.414 1904 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1540 helix: -0.30 (0.19), residues: 656 sheet: -3.93 (0.31), residues: 172 loop : -2.23 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.004 0.001 HIS B 312 PHE 0.012 0.001 PHE B 180 TYR 0.018 0.001 TYR A 421 ARG 0.002 0.000 ARG A 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 10) link_NAG-ASN : angle 3.82037 ( 30) link_BETA1-4 : bond 0.00554 ( 4) link_BETA1-4 : angle 2.81879 ( 12) hydrogen bonds : bond 0.03397 ( 498) hydrogen bonds : angle 5.13721 ( 1422) SS BOND : bond 0.00210 ( 18) SS BOND : angle 1.44264 ( 36) covalent geometry : bond 0.00208 (10424) covalent geometry : angle 0.51965 (14320) *********************** 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 22 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.659 Fit side-chains REVERT: B 184 LEU cc_start: 0.9283 (mt) cc_final: 0.8765 (mt) REVERT: B 197 MET cc_start: 0.9386 (mmm) cc_final: 0.9061 (mmm) REVERT: B 307 MET cc_start: 0.9040 (mmp) cc_final: 0.8609 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1111 time to fit residues: 4.5072 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 : 0.603 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 0.0060 chunk 86 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 0.0040 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8210 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.038656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.030205 restraints weight = 68336.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.030716 restraints weight = 49514.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031113 restraints weight = 39418.545| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.047045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.044243 restraints weight = 315.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.045243 restraints weight = 156.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.046187 restraints weight = 95.030| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10456 Z= 0.099 Angle : 0.523 9.157 14398 Z= 0.266 Chirality : 0.045 0.345 1760 Planarity : 0.003 0.026 1904 Dihedral : 7.214 58.146 1904 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1540 helix: 0.09 (0.20), residues: 674 sheet: -3.70 (0.34), residues: 172 loop : -2.10 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.002 0.000 HIS B 338 PHE 0.011 0.001 PHE A 68 TYR 0.016 0.001 TYR A 421 ARG 0.001 0.000 ARG A 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 10) link_NAG-ASN : angle 3.68981 ( 30) link_BETA1-4 : bond 0.00577 ( 4) link_BETA1-4 : angle 2.58413 ( 12) hydrogen bonds : bond 0.03064 ( 498) hydrogen bonds : angle 4.74799 ( 1422) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.42207 ( 36) covalent geometry : bond 0.00204 (10424) covalent geometry : angle 0.48549 (14320) *********************** 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 18 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.580 Fit side-chains REVERT: B 307 MET cc_start: 0.9134 (mmp) cc_final: 0.8895 (mmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1109 time to fit residues: 3.7459 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 : 0.651 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 44 optimal weight: 0.0020 chunk 47 optimal weight: 0.3980 chunk 96 optimal weight: 0.0270 chunk 111 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 126 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.039382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030715 restraints weight = 67786.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031271 restraints weight = 48765.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.031677 restraints weight = 38623.901| |-----------------------------------------------------------------------------| r_work (final): 0.2891 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.048101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.045526 restraints weight = 390.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.046661 restraints weight = 164.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047736 restraints weight = 91.066| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10456 Z= 0.085 Angle : 0.499 8.956 14398 Z= 0.250 Chirality : 0.045 0.338 1760 Planarity : 0.002 0.024 1904 Dihedral : 6.186 56.299 1904 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1540 helix: 0.40 (0.20), residues: 668 sheet: -3.58 (0.34), residues: 174 loop : -2.06 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.002 0.000 HIS B 312 PHE 0.011 0.001 PHE B 68 TYR 0.015 0.001 TYR B 421 ARG 0.001 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 10) link_NAG-ASN : angle 3.54427 ( 30) link_BETA1-4 : bond 0.00783 ( 4) link_BETA1-4 : angle 2.37957 ( 12) hydrogen bonds : bond 0.02764 ( 498) hydrogen bonds : angle 4.40256 ( 1422) SS BOND : bond 0.00321 ( 18) SS BOND : angle 1.01809 ( 36) covalent geometry : bond 0.00168 (10424) covalent geometry : angle 0.46590 (14320) *********************** 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 19 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1308 time to fit residues: 4.5464 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 : 0.778 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 87 optimal weight: 40.0000 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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** 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 = 0.3145 r_free = 0.3145 target = 0.037877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.029540 restraints weight = 69029.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.030062 restraints weight = 50895.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.030420 restraints weight = 40642.477| |-----------------------------------------------------------------------------| r_work (final): 0.2852 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.033147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.032266 restraints weight = 587.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.032686 restraints weight = 200.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.032892 restraints weight = 87.328| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10456 Z= 0.162 Angle : 0.540 9.185 14398 Z= 0.280 Chirality : 0.045 0.335 1760 Planarity : 0.003 0.024 1904 Dihedral : 5.866 56.019 1904 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1540 helix: 0.59 (0.20), residues: 676 sheet: -3.58 (0.32), residues: 184 loop : -1.87 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 338 PHE 0.009 0.001 PHE B 522 TYR 0.015 0.001 TYR A 421 ARG 0.002 0.000 ARG B 520 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 10) link_NAG-ASN : angle 3.56560 ( 30) link_BETA1-4 : bond 0.00250 ( 4) link_BETA1-4 : angle 2.27175 ( 12) hydrogen bonds : bond 0.02952 ( 498) hydrogen bonds : angle 4.37100 ( 1422) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.46047 ( 36) covalent geometry : bond 0.00320 (10424) covalent geometry : angle 0.50700 (14320) *********************** 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 13 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.689 Fit side-chains REVERT: B 307 MET cc_start: 0.9021 (mmp) cc_final: 0.8604 (mmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1136 time to fit residues: 3.0895 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 : 0.633 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 108 optimal weight: 0.3980 chunk 128 optimal weight: 0.0170 chunk 136 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 50.0000 chunk 132 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 124 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.038530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.030104 restraints weight = 67299.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.030624 restraints weight = 49874.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.030982 restraints weight = 39937.519| |-----------------------------------------------------------------------------| r_work (final): 0.2873 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.047957 restraints weight = 288.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049231 restraints weight = 136.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.049707 restraints weight = 64.373| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3299 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= 0.087 Angle : 0.496 8.893 14398 Z= 0.248 Chirality : 0.044 0.331 1760 Planarity : 0.003 0.029 1904 Dihedral : 5.505 55.569 1904 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1540 helix: 0.81 (0.20), residues: 668 sheet: -3.69 (0.34), residues: 166 loop : -2.02 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS A 192 PHE 0.009 0.001 PHE B 68 TYR 0.015 0.001 TYR A 421 ARG 0.001 0.000 ARG B 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 10) link_NAG-ASN : angle 3.49594 ( 30) link_BETA1-4 : bond 0.00613 ( 4) link_BETA1-4 : angle 2.44972 ( 12) hydrogen bonds : bond 0.02635 ( 498) hydrogen bonds : angle 4.20662 ( 1422) SS BOND : bond 0.00128 ( 18) SS BOND : angle 1.05354 ( 36) covalent geometry : bond 0.00177 (10424) covalent geometry : angle 0.46219 (14320) *********************** 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 : 0.713 Fit side-chains REVERT: B 307 MET cc_start: 0.9071 (mmp) cc_final: 0.8531 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1625 time to fit residues: 4.3161 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 : 0.630 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 0.7980 chunk 141 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 0.0010 chunk 142 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.038843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030336 restraints weight = 68133.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.030870 restraints weight = 49762.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031223 restraints weight = 39808.163| |-----------------------------------------------------------------------------| r_work (final): 0.2877 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.033076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.032388 restraints weight = 589.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.032736 restraints weight = 173.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.032894 restraints weight = 73.432| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3619 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= 0.079 Angle : 0.481 8.806 14398 Z= 0.238 Chirality : 0.044 0.328 1760 Planarity : 0.002 0.027 1904 Dihedral : 5.296 55.581 1904 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1540 helix: 0.97 (0.20), residues: 668 sheet: -3.31 (0.34), residues: 180 loop : -1.88 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.002 0.000 HIS B 192 PHE 0.008 0.001 PHE B 68 TYR 0.015 0.001 TYR B 421 ARG 0.001 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 10) link_NAG-ASN : angle 3.43713 ( 30) link_BETA1-4 : bond 0.00576 ( 4) link_BETA1-4 : angle 2.29005 ( 12) hydrogen bonds : bond 0.02408 ( 498) hydrogen bonds : angle 3.99293 ( 1422) SS BOND : bond 0.00137 ( 18) SS BOND : angle 0.95519 ( 36) covalent geometry : bond 0.00163 (10424) covalent geometry : angle 0.44898 (14320) *********************** 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 17 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.603 Fit side-chains REVERT: B 307 MET cc_start: 0.9098 (mmp) cc_final: 0.8755 (mmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1094 time to fit residues: 3.5269 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 : 0.555 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.0170 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.039094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030500 restraints weight = 67138.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031037 restraints weight = 49036.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.031411 restraints weight = 39241.896| |-----------------------------------------------------------------------------| r_work (final): 0.2890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.033734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.032972 restraints weight = 605.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.033348 restraints weight = 189.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.033510 restraints weight = 82.716| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.026 10456 Z= 0.073 Angle : 0.484 10.392 14398 Z= 0.235 Chirality : 0.044 0.323 1760 Planarity : 0.002 0.027 1904 Dihedral : 5.152 55.694 1904 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1540 helix: 0.94 (0.20), residues: 682 sheet: -3.22 (0.36), residues: 176 loop : -1.78 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS B 312 PHE 0.009 0.001 PHE B 68 TYR 0.013 0.001 TYR B 421 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 10) link_NAG-ASN : angle 3.40249 ( 30) link_BETA1-4 : bond 0.00614 ( 4) link_BETA1-4 : angle 2.27447 ( 12) hydrogen bonds : bond 0.02288 ( 498) hydrogen bonds : angle 3.86606 ( 1422) SS BOND : bond 0.00109 ( 18) SS BOND : angle 0.84669 ( 36) covalent geometry : bond 0.00147 (10424) covalent geometry : angle 0.45248 (14320) *********************** 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 16 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: B 267 ILE cc_start: 0.9536 (mt) cc_final: 0.9327 (mm) REVERT: B 307 MET cc_start: 0.9135 (mmp) cc_final: 0.8794 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1086 time to fit residues: 3.4397 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 : 0.593 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.038872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.030398 restraints weight = 68259.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.030914 restraints weight = 50323.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.031281 restraints weight = 40587.516| |-----------------------------------------------------------------------------| r_work (final): 0.2884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.035207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.032780 restraints weight = 449.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.033398 restraints weight = 209.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.033737 restraints weight = 118.813| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10456 Z= 0.075 Angle : 0.467 8.698 14398 Z= 0.231 Chirality : 0.043 0.321 1760 Planarity : 0.002 0.028 1904 Dihedral : 5.101 55.473 1904 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1540 helix: 1.10 (0.20), residues: 682 sheet: -3.28 (0.34), residues: 186 loop : -1.76 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 352 HIS 0.002 0.000 HIS B 312 PHE 0.008 0.001 PHE A 68 TYR 0.013 0.001 TYR B 421 ARG 0.002 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 10) link_NAG-ASN : angle 3.37862 ( 30) link_BETA1-4 : bond 0.00590 ( 4) link_BETA1-4 : angle 2.15517 ( 12) hydrogen bonds : bond 0.02204 ( 498) hydrogen bonds : angle 3.76769 ( 1422) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.93485 ( 36) covalent geometry : bond 0.00152 (10424) covalent geometry : angle 0.43504 (14320) ********************** 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 15 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.655 Fit side-chains REVERT: B 307 MET cc_start: 0.9164 (mmp) cc_final: 0.8839 (mmm) REVERT: B 473 MET cc_start: 0.8185 (mpp) cc_final: 0.7868 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1069 time to fit residues: 3.1866 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 : 0.594 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 0.0770 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 429 HIS ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3124 r_free = 0.3124 target = 0.037061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028869 restraints weight = 71113.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.029391 restraints weight = 51483.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029660 restraints weight = 40943.151| |-----------------------------------------------------------------------------| r_work (final): 0.2827 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.033021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.032129 restraints weight = 567.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.032469 restraints weight = 201.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.032639 restraints weight = 106.668| |-----------------------------------------------------------------------------| r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10456 Z= 0.197 Angle : 0.563 8.726 14398 Z= 0.297 Chirality : 0.045 0.336 1760 Planarity : 0.003 0.031 1904 Dihedral : 5.609 55.939 1904 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1540 helix: 0.84 (0.20), residues: 672 sheet: -3.72 (0.32), residues: 188 loop : -1.83 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.004 0.001 HIS A 338 PHE 0.017 0.002 PHE A 76 TYR 0.013 0.001 TYR A 435 ARG 0.006 0.001 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 10) link_NAG-ASN : angle 3.41487 ( 30) link_BETA1-4 : bond 0.00006 ( 4) link_BETA1-4 : angle 2.15162 ( 12) hydrogen bonds : bond 0.02856 ( 498) hydrogen bonds : angle 4.05067 ( 1422) SS BOND : bond 0.00543 ( 18) SS BOND : angle 1.47727 ( 36) covalent geometry : bond 0.00386 (10424) covalent geometry : angle 0.53422 (14320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.61 seconds wall clock time: 53 minutes 4.17 seconds (3184.17 seconds total)