Starting phenix.real_space_refine on Fri Feb 14 16:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtw_30856/02_2025/7dtw_30856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtw_30856/02_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_30856/02_2025/7dtw_30856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtw_30856/02_2025/7dtw_30856.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtw_30856/02_2025/7dtw_30856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtw_30856/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.13, 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: 2.72 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: 1.05 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: 3.39 Time building geometry restraints manager: 3.18 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: 1.850 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.060 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- 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 10424 Z= 0.510 Angle : 1.008 11.197 14320 Z= 0.570 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 *********************** 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 : 0.622 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1855 time to fit residues: 5.6054 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 : 0.750 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=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 = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.029544 restraints weight = 69602.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.030064 restraints weight = 50406.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.030447 restraints weight = 39842.805| |-----------------------------------------------------------------------------| 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 = 0.034620 restraints weight = 709.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.034646 restraints weight = 27.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.034640 restraints weight = 2.568 | |-----------------------------------------------------------------------------| r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10424 Z= 0.205 Angle : 0.619 6.961 14320 Z= 0.335 Chirality : 0.047 0.378 1760 Planarity : 0.004 0.035 1904 Dihedral : 8.366 58.210 1904 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -0.97 (0.18), residues: 660 sheet: -3.63 (0.34), residues: 142 loop : -2.57 (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 B 421 ARG 0.003 0.001 ARG A 69 *********************** 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 : 0.612 Fit side-chains REVERT: B 197 MET cc_start: 0.9456 (mmm) cc_final: 0.9211 (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: 0.1149 time to fit residues: 3.9379 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 : 0.568 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: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 20.0000 chunk 92 optimal weight: 0.0040 chunk 91 optimal weight: 0.0970 chunk 148 optimal weight: 0.0670 chunk 4 optimal weight: 0.0050 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.1742 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target = 0.038823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.030281 restraints weight = 67017.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030830 restraints weight = 47972.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031238 restraints weight = 37776.093| |-----------------------------------------------------------------------------| r_work (final): 0.2872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.046693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.044226 restraints weight = 418.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045270 restraints weight = 163.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.045864 restraints weight = 88.631| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10424 Z= 0.148 Angle : 0.527 6.622 14320 Z= 0.278 Chirality : 0.046 0.369 1760 Planarity : 0.003 0.029 1904 Dihedral : 7.578 58.262 1904 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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: -2.46 (0.21), residues: 1540 helix: -0.32 (0.19), residues: 656 sheet: -4.10 (0.33), residues: 150 loop : -2.32 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.003 0.001 HIS B 312 PHE 0.011 0.001 PHE A 68 TYR 0.017 0.001 TYR B 421 ARG 0.002 0.000 ARG B 441 *********************** 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 23 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.638 Fit side-chains REVERT: B 197 MET cc_start: 0.9364 (mmm) cc_final: 0.9042 (mmm) REVERT: B 307 MET cc_start: 0.9014 (mmp) cc_final: 0.8720 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1072 time to fit residues: 4.3262 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 : 0.569 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: 0.0020 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 120 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.038458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030000 restraints weight = 68690.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.030527 restraints weight = 49542.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030911 restraints weight = 39391.201| |-----------------------------------------------------------------------------| r_work (final): 0.2867 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.044243 restraints weight = 383.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.045287 restraints weight = 173.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046137 restraints weight = 95.717| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10424 Z= 0.139 Angle : 0.493 5.852 14320 Z= 0.263 Chirality : 0.045 0.348 1760 Planarity : 0.003 0.026 1904 Dihedral : 7.140 58.192 1904 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -1.97 (0.21), residues: 1540 helix: 0.12 (0.20), residues: 674 sheet: -3.80 (0.32), residues: 172 loop : -2.06 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 293 HIS 0.002 0.001 HIS B 338 PHE 0.008 0.001 PHE B 65 TYR 0.017 0.001 TYR A 421 ARG 0.002 0.000 ARG A 185 *********************** 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 16 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.629 Fit side-chains REVERT: B 307 MET cc_start: 0.8989 (mmp) cc_final: 0.8787 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1081 time to fit residues: 3.3606 Evaluate side-chains 11 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.617 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 44 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 96 optimal weight: 0.0170 chunk 111 optimal weight: 0.0030 chunk 87 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 91 optimal weight: 0.0060 overall best weight: 0.1242 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.039631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030963 restraints weight = 67289.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.031512 restraints weight = 48939.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.031915 restraints weight = 38892.547| |-----------------------------------------------------------------------------| r_work (final): 0.2898 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.045097 restraints weight = 393.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046230 restraints weight = 170.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047226 restraints weight = 101.265| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10424 Z= 0.109 Angle : 0.475 6.072 14320 Z= 0.245 Chirality : 0.045 0.340 1760 Planarity : 0.003 0.025 1904 Dihedral : 5.946 56.749 1904 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -1.79 (0.22), residues: 1540 helix: 0.35 (0.20), residues: 668 sheet: -3.56 (0.34), residues: 174 loop : -2.07 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.002 0.000 HIS B 312 PHE 0.012 0.001 PHE B 68 TYR 0.015 0.001 TYR A 421 ARG 0.001 0.000 ARG B 441 *********************** 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 21 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.572 Fit side-chains REVERT: B 184 LEU cc_start: 0.9322 (mt) cc_final: 0.9027 (mt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1084 time to fit residues: 4.0435 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 : 0.525 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: 0.0020 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: 6.9990 chunk 28 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 87 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 80 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.038074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029679 restraints weight = 68733.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030175 restraints weight = 50262.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.030515 restraints weight = 40419.146| |-----------------------------------------------------------------------------| r_work (final): 0.2855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.033666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.032838 restraints weight = 573.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.033240 restraints weight = 187.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.033433 restraints weight = 83.928| |-----------------------------------------------------------------------------| r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10424 Z= 0.181 Angle : 0.491 6.019 14320 Z= 0.263 Chirality : 0.044 0.333 1760 Planarity : 0.003 0.025 1904 Dihedral : 5.636 55.912 1904 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -1.37 (0.22), residues: 1540 helix: 0.77 (0.21), residues: 664 sheet: -3.47 (0.32), residues: 184 loop : -1.84 (0.25), residues: 692 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 0.011 0.001 PHE A 38 TYR 0.015 0.001 TYR A 421 ARG 0.002 0.000 ARG A 520 *********************** 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 14 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.595 Fit side-chains REVERT: B 307 MET cc_start: 0.9047 (mmp) cc_final: 0.8639 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1048 time to fit residues: 2.9317 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 : 0.523 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: 0.0024 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 64 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 34 optimal weight: 0.0030 chunk 141 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 124 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 overall best weight: 1.2150 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.038555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.030083 restraints weight = 68259.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030597 restraints weight = 49697.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.030996 restraints weight = 39682.383| |-----------------------------------------------------------------------------| r_work (final): 0.2868 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.050303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048018 restraints weight = 289.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049241 restraints weight = 134.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049684 restraints weight = 63.395| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10424 Z= 0.117 Angle : 0.455 5.467 14320 Z= 0.238 Chirality : 0.044 0.333 1760 Planarity : 0.002 0.028 1904 Dihedral : 5.478 55.725 1904 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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: -1.38 (0.22), residues: 1540 helix: 0.86 (0.20), residues: 668 sheet: -3.64 (0.34), residues: 166 loop : -1.99 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 293 HIS 0.001 0.000 HIS B 338 PHE 0.009 0.001 PHE B 68 TYR 0.015 0.001 TYR A 421 ARG 0.001 0.000 ARG B 185 *********************** 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 15 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.671 Fit side-chains REVERT: B 197 MET cc_start: 0.9374 (mmm) cc_final: 0.9122 (mmm) REVERT: B 307 MET cc_start: 0.9027 (mmp) cc_final: 0.8653 (mmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1110 time to fit residues: 3.4185 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 : 0.573 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 74 optimal weight: 0.0020 chunk 142 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.038696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030269 restraints weight = 68137.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.030787 restraints weight = 50045.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031134 restraints weight = 40304.516| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.035531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.033136 restraints weight = 434.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.033739 restraints weight = 206.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.034109 restraints weight = 117.928| |-----------------------------------------------------------------------------| r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10424 Z= 0.109 Angle : 0.445 6.671 14320 Z= 0.231 Chirality : 0.044 0.326 1760 Planarity : 0.002 0.028 1904 Dihedral : 5.247 55.783 1904 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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: -1.10 (0.23), residues: 1540 helix: 1.04 (0.20), residues: 670 sheet: -3.35 (0.35), residues: 168 loop : -1.83 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.002 0.001 HIS A 338 PHE 0.008 0.001 PHE B 68 TYR 0.015 0.001 TYR A 421 ARG 0.002 0.000 ARG B 441 *********************** 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 14 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.635 Fit side-chains REVERT: B 197 MET cc_start: 0.9351 (mmm) cc_final: 0.9102 (mmm) REVERT: B 307 MET cc_start: 0.9138 (mmp) cc_final: 0.8669 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1122 time to fit residues: 3.1664 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 : 0.556 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: 0.0024 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 : 0.003 ------------------------------------------------------------------------------- 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: 0.0040 chunk 5 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 149 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.038569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.029921 restraints weight = 67983.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030508 restraints weight = 48205.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.030923 restraints weight = 37730.848| |-----------------------------------------------------------------------------| r_work (final): 0.2869 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.032876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.032201 restraints weight = 574.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.032527 restraints weight = 165.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.032692 restraints weight = 70.896| |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10424 Z= 0.111 Angle : 0.431 5.391 14320 Z= 0.225 Chirality : 0.043 0.325 1760 Planarity : 0.002 0.029 1904 Dihedral : 5.198 55.696 1904 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.23), residues: 1540 helix: 1.07 (0.20), residues: 682 sheet: -3.33 (0.35), residues: 176 loop : -1.81 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 352 HIS 0.002 0.001 HIS A 338 PHE 0.008 0.001 PHE A 68 TYR 0.014 0.001 TYR A 421 ARG 0.001 0.000 ARG B 66 *********************** 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 14 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.534 Fit side-chains REVERT: B 307 MET cc_start: 0.9002 (mmp) cc_final: 0.8626 (mmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1020 time to fit residues: 2.8120 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 : 0.527 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 25 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 123 optimal weight: 0.0870 chunk 20 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.039194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030562 restraints weight = 67306.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031115 restraints weight = 49264.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031496 restraints weight = 39195.602| |-----------------------------------------------------------------------------| r_work (final): 0.2892 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.033279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.032478 restraints weight = 666.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.032833 restraints weight = 182.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.032993 restraints weight = 81.769| |-----------------------------------------------------------------------------| r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 10424 Z= 0.096 Angle : 0.435 5.743 14320 Z= 0.222 Chirality : 0.044 0.316 1760 Planarity : 0.002 0.028 1904 Dihedral : 5.116 55.869 1904 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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: -0.99 (0.23), residues: 1540 helix: 1.19 (0.20), residues: 670 sheet: -3.17 (0.35), residues: 182 loop : -1.84 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.001 0.000 HIS B 312 PHE 0.009 0.001 PHE A 68 TYR 0.016 0.001 TYR B 421 ARG 0.001 0.000 ARG B 69 ********************** 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 17 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.546 Fit side-chains REVERT: B 267 ILE cc_start: 0.9522 (mt) cc_final: 0.9312 (mm) REVERT: B 307 MET cc_start: 0.9102 (mmp) cc_final: 0.8626 (mmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1082 time to fit residues: 3.5178 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 : 0.574 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: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 0.3980 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 0.0030 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.0270 chunk 130 optimal weight: 30.0000 chunk 113 optimal weight: 0.0270 chunk 132 optimal weight: 9.9990 overall best weight: 0.1906 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.039239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030583 restraints weight = 68169.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.031137 restraints weight = 49246.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.031499 restraints weight = 39229.377| |-----------------------------------------------------------------------------| r_work (final): 0.2895 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.032086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.031442 restraints weight = 547.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.031731 restraints weight = 162.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.031881 restraints weight = 70.443| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 10424 Z= 0.092 Angle : 0.421 5.150 14320 Z= 0.215 Chirality : 0.043 0.314 1760 Planarity : 0.002 0.028 1904 Dihedral : 5.013 55.822 1904 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.51 % 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: -0.94 (0.22), residues: 1540 helix: 1.25 (0.20), residues: 670 sheet: -3.07 (0.35), residues: 186 loop : -1.83 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.001 0.000 HIS B 312 PHE 0.008 0.001 PHE A 68 TYR 0.014 0.001 TYR B 421 ARG 0.002 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.50 seconds wall clock time: 41 minutes 35.03 seconds (2495.03 seconds total)