Starting phenix.real_space_refine on Fri Jul 3 08:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd5_30644/07_2026/7dd5_30644.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.082 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 4 4.86 5 C 8303 2.51 5 N 2049 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12810 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6247 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 34, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6269 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 33, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 91 Unusual residues: {' CA': 4, ' CL': 1, 'NAG': 3, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1108 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {' CA': 2, ' CL': 1, 'NAG': 3, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.18 Number of scatterers: 12810 At special positions: 0 Unit cell: (100.386, 93.288, 181.506, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 4 17.00 S 70 16.00 O 2378 8.00 N 2049 7.00 C 8303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.19 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=1.82 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 764 " 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=1, 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 A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 399 " " NAG A1107 " - " ASN A 467 " " NAG B1104 " - " ASN B 287 " " NAG B1105 " - " ASN B 399 " " NAG B1106 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 528.3 milliseconds 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 18 sheets defined 48.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.922A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.775A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.731A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.005A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.022A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.516A pdb=" N VAL A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.905A pdb=" N GLY A 531 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 636 Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.763A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 664 through 668 removed outlier: 4.278A pdb=" N ILE A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 697 removed outlier: 3.724A pdb=" N CYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 720 through 743 removed outlier: 3.910A pdb=" N PHE A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 743 " --> pdb=" O VAL A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 793 removed outlier: 3.763A pdb=" N LEU A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 825 removed outlier: 4.124A pdb=" N PHE A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Proline residue: A 822 - end of helix Processing helix chain 'A' and resid 828 through 861 removed outlier: 3.880A pdb=" N SER A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 855 " --> pdb=" O ILE 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: 3.846A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.994A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.682A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.743A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.831A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.579A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.570A pdb=" N HIS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 636 Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.865A pdb=" N SER B 664 " --> pdb=" O CYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 668 removed outlier: 3.881A pdb=" N ILE B 668 " --> pdb=" O LEU B 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 672 through 697 removed outlier: 3.666A pdb=" N CYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 720 through 744 removed outlier: 4.172A pdb=" N PHE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 793 removed outlier: 3.561A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 825 removed outlier: 3.777A pdb=" N PHE B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 828 through 862 removed outlier: 3.778A pdb=" N SER B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.056A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.823A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.839A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP A 293 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N PHE A 320 " --> pdb=" O TRP A 293 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA A 295 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR A 488 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N HIS A 509 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 490 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 467 through 470 Processing sheet with id=AA6, first strand: chain 'A' and resid 549 through 553 Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA9, first strand: chain 'A' and resid 601 through 603 removed outlier: 7.176A pdb=" N GLN A 601 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ILE A 762 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU A 603 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N CYS A 764 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.977A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.872A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.053A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.780A pdb=" N TYR B 488 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N HIS B 509 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 490 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB6, first strand: chain 'B' and resid 549 through 552 Processing sheet with id=AB7, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AB8, first strand: chain 'B' and resid 588 through 589 Processing sheet with id=AB9, first strand: chain 'B' and resid 748 through 752 591 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2068 1.27 - 1.41: 3464 1.41 - 1.55: 7505 1.55 - 1.69: 0 1.69 - 1.83: 88 Bond restraints: 13125 Sorted by residual: bond pdb=" C19 YP1 B1108 " pdb=" C24 YP1 B1108 " ideal model delta sigma weight residual 1.418 1.528 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C19 YP1 A1109 " pdb=" C24 YP1 A1109 " ideal model delta sigma weight residual 1.418 1.528 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C7 NAG A1107 " pdb=" N2 NAG A1107 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C7 NAG B1104 " pdb=" N2 NAG B1104 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B1106 " pdb=" N2 NAG B1106 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 13120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17340 2.00 - 4.01: 393 4.01 - 6.01: 80 6.01 - 8.01: 16 8.01 - 10.01: 1 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N LYS B 697 " pdb=" CA LYS B 697 " pdb=" C LYS B 697 " ideal model delta sigma weight residual 113.20 108.35 4.85 1.36e+00 5.41e-01 1.27e+01 angle pdb=" CA ARG A 700 " pdb=" C ARG A 700 " pdb=" O ARG A 700 " ideal model delta sigma weight residual 122.13 118.28 3.85 1.13e+00 7.83e-01 1.16e+01 angle pdb=" C ALA A 144 " pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sigma weight residual 109.38 119.39 -10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N VAL A 507 " pdb=" CA VAL A 507 " pdb=" C VAL A 507 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 7265 29.58 - 59.17: 313 59.17 - 88.75: 24 88.75 - 118.34: 6 118.34 - 147.92: 4 Dihedral angle restraints: 7612 sinusoidal: 2962 harmonic: 4650 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 545 " pdb=" SG CYS A 545 " pdb=" SG CYS A 564 " pdb=" CB CYS A 564 " ideal model delta sinusoidal sigma weight residual -86.00 -157.76 71.76 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" C15 YP1 B1108 " pdb=" C16 YP1 B1108 " pdb=" C17 YP1 B1108 " pdb=" O1 YP1 B1108 " ideal model delta sinusoidal sigma weight residual 136.97 -75.11 -147.92 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 7609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1956 0.111 - 0.221: 65 0.221 - 0.332: 1 0.332 - 0.442: 0 0.442 - 0.553: 1 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C1 NAG A1107 " pdb=" ND2 ASN A 467 " pdb=" C2 NAG A1107 " pdb=" O5 NAG A1107 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2020 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 727 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C VAL B 727 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL B 727 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE B 728 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 670 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 671 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 671 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 671 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 405 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO B 406 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 406 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 406 " -0.021 5.00e-02 4.00e+02 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 175 2.57 - 3.15: 11283 3.15 - 3.73: 19656 3.73 - 4.32: 26990 4.32 - 4.90: 43479 Nonbonded interactions: 101583 Sorted by model distance: nonbonded pdb=" OE1 GLU A 836 " pdb=" O2 YP1 A1109 " model vdw 1.985 3.040 nonbonded pdb=" OE2 GLU B 836 " pdb=" O2 YP1 B1108 " model vdw 2.080 3.040 nonbonded pdb=" CD2 TYR A 824 " pdb=" CG1 VAL A 832 " model vdw 2.138 3.760 nonbonded pdb=" N GLU B 498 " pdb=" OE1 GLU B 498 " model vdw 2.146 3.120 nonbonded pdb=" OG1 THR A 395 " pdb=" OD1 ASP A 397 " model vdw 2.188 3.040 ... (remaining 101578 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' and (resid 22 through 119 or resid 136 through 600 or (resid 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 1103 o \ r resid 1105 through 1106 or resid 1108 through 1109)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 1103 o \ r resid 1105 through 1108)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.010 0.600 13157 Z= 0.700 Angle : 0.770 14.666 17906 Z= 0.417 Chirality : 0.048 0.553 2023 Planarity : 0.004 0.039 2248 Dihedral : 16.659 147.922 4549 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.15 % Allowed : 20.28 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.18), residues: 1581 helix: -1.13 (0.17), residues: 706 sheet: -2.81 (0.34), residues: 180 loop : -2.90 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 265 TYR 0.011 0.001 TYR B 857 PHE 0.012 0.001 PHE A 667 TRP 0.009 0.001 TRP B 299 HIS 0.004 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.45 (13125) covalent geometry : angle 0.75037 / 0.41 (17830) SS BOND : bond 0.06453 / 4.11 ( 17) SS BOND : angle 2.29650 / 1.58 ( 34) hydrogen bonds : bond 0.13931 / 9.50 ( 587) hydrogen bonds : angle 6.15727 / 4.27 ( 1710) Misc. bond : bond 0.59997 / 31.58 ( 1) link_BETA1-4 : bond 0.00288 / 0.14 ( 4) link_BETA1-4 : angle 1.09311 / 0.67 ( 12) link_NAG-ASN : bond 0.00375 / 0.20 ( 10) link_NAG-ASN : angle 3.55239 / 3.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6644 (mt-10) REVERT: A 254 GLN cc_start: 0.8319 (mt0) cc_final: 0.8003 (tp40) REVERT: A 587 ASP cc_start: 0.9138 (m-30) cc_final: 0.8405 (m-30) REVERT: A 588 TYR cc_start: 0.9036 (m-80) cc_final: 0.8754 (m-80) REVERT: A 752 ASN cc_start: 0.8897 (t0) cc_final: 0.8558 (t0) REVERT: A 759 ILE cc_start: 0.7590 (mt) cc_final: 0.7218 (mt) REVERT: A 820 PHE cc_start: 0.7593 (t80) cc_final: 0.7350 (t80) REVERT: B 52 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8860 (mtpp) REVERT: B 202 GLU cc_start: 0.7921 (tt0) cc_final: 0.7547 (tt0) REVERT: B 205 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7286 (mmt180) REVERT: B 229 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 248 ASP cc_start: 0.8255 (m-30) cc_final: 0.8032 (m-30) REVERT: B 253 GLN cc_start: 0.8081 (mt0) cc_final: 0.7725 (tt0) REVERT: B 498 GLU cc_start: 0.8633 (pm20) cc_final: 0.8426 (pm20) REVERT: B 499 ASP cc_start: 0.8501 (t70) cc_final: 0.8208 (m-30) REVERT: B 753 HIS cc_start: 0.8720 (p-80) cc_final: 0.8298 (p-80) REVERT: B 762 ILE cc_start: 0.8629 (mt) cc_final: 0.8338 (tp) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.0995 time to fit residues: 31.4547 Evaluate side-chains 128 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 193 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN A 646 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 193 GLN B 245 GLN B 260 GLN B 335 GLN B 465 HIS B 765 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091685 restraints weight = 24203.080| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.25 r_work: 0.3119 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13157 Z= 0.168 Angle : 0.681 16.009 17906 Z= 0.333 Chirality : 0.049 0.644 2023 Planarity : 0.004 0.043 2248 Dihedral : 11.104 175.205 1729 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.01 % Allowed : 20.13 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.20), residues: 1581 helix: 0.05 (0.18), residues: 712 sheet: -2.40 (0.35), residues: 192 loop : -2.20 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 312 TYR 0.014 0.001 TYR B 588 PHE 0.024 0.001 PHE A 661 TRP 0.009 0.001 TRP A 741 HIS 0.005 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (13125) covalent geometry : angle 0.66109 / 0.33 (17830) SS BOND : bond 0.00271 / 0.18 ( 17) SS BOND : angle 0.85581 / 0.56 ( 34) hydrogen bonds : bond 0.05408 / 3.53 ( 587) hydrogen bonds : angle 5.01769 / 3.46 ( 1710) Misc. bond : bond 0.01088 / 0.57 ( 1) link_BETA1-4 : bond 0.00653 / 0.32 ( 4) link_BETA1-4 : angle 1.43232 / 0.80 ( 12) link_NAG-ASN : bond 0.00446 / 0.26 ( 10) link_NAG-ASN : angle 3.89199 / 3.35 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8779 (tpp) cc_final: 0.8188 (mmt) REVERT: A 191 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 202 GLU cc_start: 0.8563 (tt0) cc_final: 0.8231 (mt-10) REVERT: A 229 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7315 (mt-10) REVERT: A 588 TYR cc_start: 0.9166 (m-80) cc_final: 0.8902 (m-80) REVERT: A 722 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 752 ASN cc_start: 0.9181 (t0) cc_final: 0.8936 (t0) REVERT: A 810 MET cc_start: 0.7985 (mtm) cc_final: 0.7044 (ttp) REVERT: A 814 PHE cc_start: 0.8250 (m-80) cc_final: 0.7192 (m-80) REVERT: B 52 LYS cc_start: 0.9269 (mtmt) cc_final: 0.9043 (mtpp) REVERT: B 202 GLU cc_start: 0.8615 (tt0) cc_final: 0.8333 (tt0) REVERT: B 205 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8140 (mmt180) REVERT: B 564 CYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8794 (m) outliers start: 54 outliers final: 31 residues processed: 186 average time/residue: 0.0806 time to fit residues: 22.7752 Evaluate side-chains 148 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 765 HIS Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 117 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN A 492 ASN A 494 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 179 GLN B 253 GLN B 335 GLN B 765 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.138961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092464 restraints weight = 24245.505| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.29 r_work: 0.3129 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13157 Z= 0.131 Angle : 0.644 15.805 17906 Z= 0.310 Chirality : 0.047 0.611 2023 Planarity : 0.004 0.049 2248 Dihedral : 10.297 154.124 1727 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.23 % Allowed : 20.65 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1581 helix: 0.64 (0.19), residues: 705 sheet: -2.02 (0.35), residues: 197 loop : -1.94 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 751 TYR 0.011 0.001 TYR B 420 PHE 0.022 0.001 PHE A 661 TRP 0.009 0.001 TRP A 741 HIS 0.005 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (13125) covalent geometry : angle 0.62523 / 0.31 (17830) SS BOND : bond 0.00318 / 0.16 ( 17) SS BOND : angle 0.75943 / 0.48 ( 34) hydrogen bonds : bond 0.04772 / 3.09 ( 587) hydrogen bonds : angle 4.67649 / 3.22 ( 1710) Misc. bond : bond 0.01269 / 0.67 ( 1) link_BETA1-4 : bond 0.00597 / 0.29 ( 4) link_BETA1-4 : angle 1.35523 / 0.72 ( 12) link_NAG-ASN : bond 0.00498 / 0.27 ( 10) link_NAG-ASN : angle 3.73657 / 3.25 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8780 (tpp) cc_final: 0.8165 (mmm) REVERT: A 191 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 202 GLU cc_start: 0.8626 (tt0) cc_final: 0.8261 (mt-10) REVERT: A 229 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7322 (mt-10) REVERT: A 588 TYR cc_start: 0.9125 (m-80) cc_final: 0.8817 (m-80) REVERT: A 814 PHE cc_start: 0.8307 (m-80) cc_final: 0.7679 (m-80) REVERT: B 50 ASP cc_start: 0.8680 (t0) cc_final: 0.8442 (t0) REVERT: B 52 LYS cc_start: 0.9270 (mtmt) cc_final: 0.9035 (mtpp) REVERT: B 202 GLU cc_start: 0.8643 (tt0) cc_final: 0.8326 (tt0) REVERT: B 205 ARG cc_start: 0.8619 (mtt90) cc_final: 0.8176 (mmt180) REVERT: B 251 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 564 CYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8767 (m) REVERT: B 770 MET cc_start: 0.6710 (tpp) cc_final: 0.6470 (tpp) outliers start: 57 outliers final: 36 residues processed: 171 average time/residue: 0.0842 time to fit residues: 22.1113 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 674 TRP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 HIS Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 765 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091787 restraints weight = 24401.462| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.26 r_work: 0.3115 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13157 Z= 0.139 Angle : 0.618 15.990 17906 Z= 0.297 Chirality : 0.046 0.588 2023 Planarity : 0.004 0.051 2248 Dihedral : 9.523 139.281 1727 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.38 % Allowed : 20.06 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1581 helix: 0.86 (0.19), residues: 706 sheet: -1.82 (0.35), residues: 197 loop : -1.77 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.012 0.001 TYR B 420 PHE 0.013 0.001 PHE A 661 TRP 0.017 0.001 TRP A 817 HIS 0.014 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (13125) covalent geometry : angle 0.59802 / 0.29 (17830) SS BOND : bond 0.00294 / 0.20 ( 17) SS BOND : angle 0.72176 / 0.47 ( 34) hydrogen bonds : bond 0.04575 / 2.97 ( 587) hydrogen bonds : angle 4.54400 / 3.12 ( 1710) Misc. bond : bond 0.00027 / 0.01 ( 1) link_BETA1-4 : bond 0.00554 / 0.27 ( 4) link_BETA1-4 : angle 1.33438 / 0.71 ( 12) link_NAG-ASN : bond 0.00438 / 0.23 ( 10) link_NAG-ASN : angle 3.70801 / 3.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7106 (t0) cc_final: 0.6753 (t0) REVERT: A 91 MET cc_start: 0.8766 (tpp) cc_final: 0.8337 (mmp) REVERT: A 191 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 202 GLU cc_start: 0.8610 (tt0) cc_final: 0.8240 (mt-10) REVERT: A 229 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7345 (mt-10) REVERT: A 588 TYR cc_start: 0.9144 (m-80) cc_final: 0.8811 (m-80) REVERT: A 750 TYR cc_start: 0.8267 (p90) cc_final: 0.7541 (p90) REVERT: A 814 PHE cc_start: 0.8346 (m-80) cc_final: 0.7648 (m-80) REVERT: B 202 GLU cc_start: 0.8666 (tt0) cc_final: 0.8347 (tt0) REVERT: B 205 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8272 (mmt180) REVERT: B 564 CYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8840 (m) REVERT: B 810 MET cc_start: 0.7375 (ptt) cc_final: 0.7120 (ptm) outliers start: 59 outliers final: 41 residues processed: 162 average time/residue: 0.0788 time to fit residues: 20.2909 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 30 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093053 restraints weight = 24341.650| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.33 r_work: 0.3139 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13157 Z= 0.110 Angle : 0.591 15.074 17906 Z= 0.285 Chirality : 0.045 0.548 2023 Planarity : 0.004 0.055 2248 Dihedral : 8.428 116.644 1727 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.71 % Allowed : 19.91 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1581 helix: 1.01 (0.19), residues: 706 sheet: -1.60 (0.36), residues: 197 loop : -1.59 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.010 0.001 TYR B 424 PHE 0.012 0.001 PHE A 845 TRP 0.013 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13125) covalent geometry : angle 0.57278 / 0.28 (17830) SS BOND : bond 0.00109 / 0.06 ( 17) SS BOND : angle 0.60367 / 0.37 ( 34) hydrogen bonds : bond 0.04173 / 2.70 ( 587) hydrogen bonds : angle 4.35037 / 2.99 ( 1710) Misc. bond : bond 0.00047 / 0.02 ( 1) link_BETA1-4 : bond 0.00658 / 0.32 ( 4) link_BETA1-4 : angle 1.28046 / 0.69 ( 12) link_NAG-ASN : bond 0.00503 / 0.27 ( 10) link_NAG-ASN : angle 3.48906 / 3.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7119 (t0) cc_final: 0.6781 (t0) REVERT: A 91 MET cc_start: 0.8797 (tpp) cc_final: 0.8366 (mmp) REVERT: A 191 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 202 GLU cc_start: 0.8596 (tt0) cc_final: 0.8234 (mt-10) REVERT: A 229 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7350 (mt-10) REVERT: A 408 MET cc_start: 0.8629 (mmt) cc_final: 0.8348 (mmt) REVERT: A 588 TYR cc_start: 0.9166 (m-80) cc_final: 0.8825 (m-80) REVERT: A 611 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4393 (t80) REVERT: A 674 TRP cc_start: 0.7548 (m-10) cc_final: 0.7314 (m-10) REVERT: A 750 TYR cc_start: 0.8312 (p90) cc_final: 0.7642 (p90) REVERT: A 810 MET cc_start: 0.7340 (mtt) cc_final: 0.7019 (mtt) REVERT: A 814 PHE cc_start: 0.8374 (m-80) cc_final: 0.7636 (m-80) REVERT: B 202 GLU cc_start: 0.8679 (tt0) cc_final: 0.8347 (tt0) REVERT: B 205 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8240 (mmt180) REVERT: B 810 MET cc_start: 0.7399 (ptt) cc_final: 0.7061 (ptm) outliers start: 50 outliers final: 37 residues processed: 161 average time/residue: 0.0740 time to fit residues: 18.7511 Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS B 117 GLN B 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.135215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088516 restraints weight = 24525.294| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.26 r_work: 0.3058 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13157 Z= 0.209 Angle : 0.643 16.533 17906 Z= 0.314 Chirality : 0.047 0.572 2023 Planarity : 0.004 0.055 2248 Dihedral : 7.439 90.224 1727 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.05 % Allowed : 19.17 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1581 helix: 1.00 (0.19), residues: 718 sheet: -1.40 (0.37), residues: 199 loop : -1.66 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.018 0.001 TYR B 420 PHE 0.013 0.001 PHE B 68 TRP 0.011 0.001 TRP A 817 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (13125) covalent geometry : angle 0.62292 / 0.31 (17830) SS BOND : bond 0.00296 / 0.21 ( 17) SS BOND : angle 0.92684 / 0.55 ( 34) hydrogen bonds : bond 0.04825 / 3.17 ( 587) hydrogen bonds : angle 4.45463 / 3.05 ( 1710) Misc. bond : bond 0.01013 / 0.53 ( 1) link_BETA1-4 : bond 0.00400 / 0.19 ( 4) link_BETA1-4 : angle 1.40346 / 0.70 ( 12) link_NAG-ASN : bond 0.00345 / 0.21 ( 10) link_NAG-ASN : angle 3.75054 / 3.34 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7281 (t0) cc_final: 0.6983 (t0) REVERT: A 91 MET cc_start: 0.8839 (tpp) cc_final: 0.8216 (mmp) REVERT: A 191 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7572 (mm-30) REVERT: A 202 GLU cc_start: 0.8672 (tt0) cc_final: 0.8380 (mt-10) REVERT: A 229 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7428 (mt-10) REVERT: A 588 TYR cc_start: 0.9155 (m-80) cc_final: 0.8803 (m-80) REVERT: A 750 TYR cc_start: 0.8302 (p90) cc_final: 0.7721 (p90) REVERT: A 810 MET cc_start: 0.7143 (mtt) cc_final: 0.6757 (mtt) REVERT: A 814 PHE cc_start: 0.8413 (m-80) cc_final: 0.7688 (m-80) REVERT: B 202 GLU cc_start: 0.8692 (tt0) cc_final: 0.8489 (tt0) REVERT: B 205 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8635 (mtt-85) REVERT: B 564 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8890 (m) REVERT: B 791 PHE cc_start: 0.8233 (t80) cc_final: 0.7927 (t80) outliers start: 68 outliers final: 46 residues processed: 173 average time/residue: 0.0839 time to fit residues: 22.7831 Evaluate side-chains 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 122 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090900 restraints weight = 24404.926| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.24 r_work: 0.3101 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13157 Z= 0.137 Angle : 0.615 15.229 17906 Z= 0.298 Chirality : 0.046 0.544 2023 Planarity : 0.004 0.055 2248 Dihedral : 6.878 79.038 1727 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.49 % Allowed : 20.65 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1581 helix: 1.07 (0.19), residues: 721 sheet: -1.31 (0.37), residues: 199 loop : -1.55 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.012 0.001 TYR B 420 PHE 0.032 0.001 PHE A 791 TRP 0.013 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13125) covalent geometry : angle 0.59404 / 0.29 (17830) SS BOND : bond 0.00127 / 0.08 ( 17) SS BOND : angle 1.58897 / 1.11 ( 34) hydrogen bonds : bond 0.04243 / 2.76 ( 587) hydrogen bonds : angle 4.31051 / 2.96 ( 1710) Misc. bond : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : bond 0.00642 / 0.31 ( 4) link_BETA1-4 : angle 1.24730 / 0.69 ( 12) link_NAG-ASN : bond 0.00407 / 0.21 ( 10) link_NAG-ASN : angle 3.50124 / 3.10 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7295 (t0) cc_final: 0.7028 (t0) REVERT: A 91 MET cc_start: 0.8816 (tpp) cc_final: 0.8192 (mmp) REVERT: A 191 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 202 GLU cc_start: 0.8633 (tt0) cc_final: 0.8258 (mt-10) REVERT: A 229 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7425 (mt-10) REVERT: A 472 MET cc_start: 0.8892 (mmm) cc_final: 0.8548 (mmp) REVERT: A 588 TYR cc_start: 0.9194 (m-80) cc_final: 0.8828 (m-80) REVERT: A 750 TYR cc_start: 0.8331 (p90) cc_final: 0.7771 (p90) REVERT: A 810 MET cc_start: 0.7111 (mtt) cc_final: 0.6752 (tpp) REVERT: B 202 GLU cc_start: 0.8702 (tt0) cc_final: 0.8369 (tt0) REVERT: B 205 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8330 (mmt180) REVERT: B 770 MET cc_start: 0.6720 (tpp) cc_final: 0.6396 (tpp) outliers start: 47 outliers final: 39 residues processed: 153 average time/residue: 0.0822 time to fit residues: 19.6556 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 63 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 0.0670 chunk 136 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.139035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092498 restraints weight = 24243.823| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.27 r_work: 0.3127 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13157 Z= 0.110 Angle : 0.589 14.320 17906 Z= 0.285 Chirality : 0.044 0.504 2023 Planarity : 0.003 0.054 2248 Dihedral : 6.565 74.258 1727 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.49 % Allowed : 20.95 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1581 helix: 1.16 (0.19), residues: 721 sheet: -1.27 (0.37), residues: 199 loop : -1.48 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.010 0.001 TYR B 420 PHE 0.018 0.001 PHE A 791 TRP 0.012 0.001 TRP A 817 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13125) covalent geometry : angle 0.57077 / 0.28 (17830) SS BOND : bond 0.00147 / 0.09 ( 17) SS BOND : angle 1.34554 / 1.20 ( 34) hydrogen bonds : bond 0.03945 / 2.56 ( 587) hydrogen bonds : angle 4.19041 / 2.88 ( 1710) Misc. bond : bond 0.00131 / 0.07 ( 1) link_BETA1-4 : bond 0.00746 / 0.36 ( 4) link_BETA1-4 : angle 1.32111 / 0.75 ( 12) link_NAG-ASN : bond 0.00645 / 0.43 ( 10) link_NAG-ASN : angle 3.27547 / 2.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7293 (t0) cc_final: 0.7036 (t0) REVERT: A 91 MET cc_start: 0.8808 (tpp) cc_final: 0.8158 (mmp) REVERT: A 202 GLU cc_start: 0.8688 (tt0) cc_final: 0.8412 (mt-10) REVERT: A 229 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7426 (mt-10) REVERT: A 472 MET cc_start: 0.8861 (mmm) cc_final: 0.8552 (mmp) REVERT: A 588 TYR cc_start: 0.9177 (m-80) cc_final: 0.8792 (m-80) REVERT: A 750 TYR cc_start: 0.8291 (p90) cc_final: 0.7728 (p90) REVERT: A 810 MET cc_start: 0.7131 (mtt) cc_final: 0.6854 (tpp) REVERT: B 202 GLU cc_start: 0.8705 (tt0) cc_final: 0.8413 (tt0) REVERT: B 205 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8401 (mmt180) REVERT: B 564 CYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8959 (m) REVERT: B 770 MET cc_start: 0.6880 (tpp) cc_final: 0.6603 (tpp) outliers start: 47 outliers final: 37 residues processed: 153 average time/residue: 0.0811 time to fit residues: 19.6526 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 137 optimal weight: 30.0000 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089507 restraints weight = 24434.321| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.26 r_work: 0.3078 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13157 Z= 0.185 Angle : 0.625 15.296 17906 Z= 0.307 Chirality : 0.046 0.524 2023 Planarity : 0.004 0.054 2248 Dihedral : 6.537 82.104 1727 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.57 % Allowed : 21.17 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1581 helix: 1.15 (0.19), residues: 721 sheet: -1.34 (0.36), residues: 212 loop : -1.55 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.015 0.001 TYR B 420 PHE 0.028 0.001 PHE B 788 TRP 0.010 0.001 TRP B 741 HIS 0.004 0.001 HIS B 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (13125) covalent geometry : angle 0.60593 / 0.30 (17830) SS BOND : bond 0.00167 / 0.11 ( 17) SS BOND : angle 1.50603 / 1.21 ( 34) hydrogen bonds : bond 0.04453 / 2.92 ( 587) hydrogen bonds : angle 4.28052 / 2.94 ( 1710) Misc. bond : bond 0.00161 / 0.08 ( 1) link_BETA1-4 : bond 0.00466 / 0.22 ( 4) link_BETA1-4 : angle 1.33909 / 0.69 ( 12) link_NAG-ASN : bond 0.00302 / 0.15 ( 10) link_NAG-ASN : angle 3.45629 / 3.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7339 (t0) cc_final: 0.7077 (t0) REVERT: A 91 MET cc_start: 0.8792 (tpp) cc_final: 0.8131 (mmp) REVERT: A 191 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 202 GLU cc_start: 0.8646 (tt0) cc_final: 0.8443 (mt-10) REVERT: A 229 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7459 (mt-10) REVERT: A 588 TYR cc_start: 0.9203 (m-80) cc_final: 0.8843 (m-80) REVERT: A 810 MET cc_start: 0.7162 (mtt) cc_final: 0.6926 (mtt) REVERT: A 814 PHE cc_start: 0.8442 (m-80) cc_final: 0.7699 (m-80) REVERT: B 202 GLU cc_start: 0.8747 (tt0) cc_final: 0.8502 (tt0) REVERT: B 564 CYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8830 (m) REVERT: B 770 MET cc_start: 0.6929 (tpp) cc_final: 0.6665 (tpp) outliers start: 48 outliers final: 42 residues processed: 146 average time/residue: 0.0823 time to fit residues: 18.7682 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 134 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.137441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.090406 restraints weight = 24331.320| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.30 r_work: 0.3097 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13157 Z= 0.145 Angle : 0.604 14.726 17906 Z= 0.294 Chirality : 0.045 0.513 2023 Planarity : 0.004 0.053 2248 Dihedral : 6.431 90.258 1727 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.34 % Allowed : 21.55 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1581 helix: 1.19 (0.19), residues: 721 sheet: -1.31 (0.36), residues: 209 loop : -1.53 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 205 TYR 0.013 0.001 TYR B 420 PHE 0.029 0.001 PHE B 788 TRP 0.012 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13125) covalent geometry : angle 0.58556 / 0.29 (17830) SS BOND : bond 0.00130 / 0.08 ( 17) SS BOND : angle 1.26317 / 1.02 ( 34) hydrogen bonds : bond 0.04171 / 2.72 ( 587) hydrogen bonds : angle 4.20938 / 2.90 ( 1710) Misc. bond : bond 0.00123 / 0.06 ( 1) link_BETA1-4 : bond 0.00659 / 0.32 ( 4) link_BETA1-4 : angle 1.27094 / 0.69 ( 12) link_NAG-ASN : bond 0.00384 / 0.21 ( 10) link_NAG-ASN : angle 3.35053 / 2.97 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7371 (t0) cc_final: 0.7135 (t0) REVERT: A 91 MET cc_start: 0.8839 (tpp) cc_final: 0.8135 (mmt) REVERT: A 191 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 202 GLU cc_start: 0.8640 (tt0) cc_final: 0.8325 (mt-10) REVERT: A 229 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7490 (mt-10) REVERT: A 588 TYR cc_start: 0.9194 (m-80) cc_final: 0.8850 (m-80) REVERT: A 810 MET cc_start: 0.7107 (mtt) cc_final: 0.6392 (tpp) REVERT: A 814 PHE cc_start: 0.8438 (m-80) cc_final: 0.7574 (m-80) REVERT: B 202 GLU cc_start: 0.8713 (tt0) cc_final: 0.8351 (tt0) REVERT: B 205 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8187 (mmt180) REVERT: B 564 CYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8790 (m) REVERT: B 770 MET cc_start: 0.6932 (tpp) cc_final: 0.6693 (tpp) outliers start: 45 outliers final: 39 residues processed: 144 average time/residue: 0.0801 time to fit residues: 17.7219 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.0060 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091036 restraints weight = 24245.065| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.28 r_work: 0.3106 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13157 Z= 0.128 Angle : 0.597 14.409 17906 Z= 0.291 Chirality : 0.045 0.503 2023 Planarity : 0.004 0.051 2248 Dihedral : 6.345 94.700 1727 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.12 % Allowed : 21.55 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1581 helix: 1.26 (0.19), residues: 721 sheet: -1.21 (0.36), residues: 209 loop : -1.47 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 205 TYR 0.012 0.001 TYR B 420 PHE 0.022 0.001 PHE A 791 TRP 0.012 0.001 TRP B 741 HIS 0.003 0.001 HIS B 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13125) covalent geometry : angle 0.57946 / 0.29 (17830) SS BOND : bond 0.00132 / 0.08 ( 17) SS BOND : angle 1.22022 / 0.98 ( 34) hydrogen bonds : bond 0.04078 / 2.67 ( 587) hydrogen bonds : angle 4.16584 / 2.87 ( 1710) Misc. bond : bond 0.00114 / 0.06 ( 1) link_BETA1-4 : bond 0.00583 / 0.28 ( 4) link_BETA1-4 : angle 1.29416 / 0.70 ( 12) link_NAG-ASN : bond 0.00403 / 0.21 ( 10) link_NAG-ASN : angle 3.27799 / 2.91 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.21 seconds wall clock time: 53 minutes 37.93 seconds (3217.93 seconds total)