Starting phenix.real_space_refine on Fri Aug 7 00:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zv9_74865/08_2026/9zv9_74865.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 11192 2.51 5 N 2955 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17756 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3926 Classifications: {'peptide': 491} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "K" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.25, per 1000 atoms: 0.24 Number of scatterers: 17756 At special positions: 0 Unit cell: (142.725, 146.025, 147.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3522 8.00 N 2955 7.00 C 11192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.02 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 498 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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=2, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 508 " " NAG A 603 " - " ASN A 33 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 508 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 508 " " NAG C 603 " - " ASN C 33 " " NAG W 1 " - " ASN B 310 " " NAG X 1 " - " ASN A 310 " " NAG Y 1 " - " ASN C 310 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 863.4 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4018 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 53 sheets defined 19.3% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 394 through 412 Processing helix chain 'A' and resid 428 through 480 removed outlier: 3.631A pdb=" N GLU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 512 through 523 removed outlier: 3.969A pdb=" N TYR A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 394 through 412 Processing helix chain 'B' and resid 428 through 481 Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.979A pdb=" N LEU B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 394 through 413 removed outlier: 3.802A pdb=" N MET C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 481 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 512 through 524 removed outlier: 3.897A pdb=" N TYR C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG C 521 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 522 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.661A pdb=" N ASN H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.661A pdb=" N ASN D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.661A pdb=" N ASN G 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 3.528A pdb=" N CYS A 14 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.405A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.030A pdb=" N LEU A 51 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N CYS A 298 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 53 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.914A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 89 " --> pdb=" O MET A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.547A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU A 189 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 266 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 271 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS A 120 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 283 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 118 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.547A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A 189 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.575A pdb=" N CYS A 146 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AB2, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB3, first strand: chain 'A' and resid 484 through 486 Processing sheet with id=AB4, first strand: chain 'B' and resid 12 through 17 Processing sheet with id=AB5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.994A pdb=" N LEU B 51 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N CYS B 298 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 53 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.832A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 89 " --> pdb=" O MET B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.453A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU B 189 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B 266 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 271 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS B 120 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 283 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 118 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.453A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 189 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 148 removed outlier: 7.853A pdb=" N ALA B 145 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N ALA B 152 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AC6, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC7, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AC9, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD2, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.988A pdb=" N LEU C 51 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N CYS C 298 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.692A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 89 " --> pdb=" O MET C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.518A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU C 189 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR C 266 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 271 " --> pdb=" O HIS C 120 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N HIS C 120 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS C 283 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 118 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.518A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 189 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AD8, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.769A pdb=" N ALA C 145 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ALA C 152 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AE1, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AE2, first strand: chain 'C' and resid 484 through 486 Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.532A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.255A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.168A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.532A pdb=" N LYS D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 80 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 70 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.255A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.168A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.532A pdb=" N LYS G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER G 70 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.255A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.168A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1770 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: 4.25 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2893 1.31 - 1.44: 5225 1.44 - 1.57: 9937 1.57 - 1.71: 4 1.71 - 1.84: 126 Bond restraints: 18185 Sorted by residual: bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.464 1.418 0.046 9.30e-03 1.16e+04 2.45e+01 bond pdb=" CA SER B 87 " pdb=" CB SER B 87 " ideal model delta sigma weight residual 1.533 1.457 0.076 1.60e-02 3.91e+03 2.25e+01 bond pdb=" C ASN C 508 " pdb=" O ASN C 508 " ideal model delta sigma weight residual 1.234 1.172 0.063 1.38e-02 5.25e+03 2.06e+01 bond pdb=" C PRO B 84 " pdb=" O PRO B 84 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.30e-02 5.92e+03 1.95e+01 bond pdb=" C PRO A 84 " pdb=" O PRO A 84 " ideal model delta sigma weight residual 1.232 1.179 0.053 1.25e-02 6.40e+03 1.83e+01 ... (remaining 18180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23780 2.35 - 4.71: 757 4.71 - 7.06: 103 7.06 - 9.41: 35 9.41 - 11.77: 13 Bond angle restraints: 24688 Sorted by residual: angle pdb=" C ASN A 94 " pdb=" CA ASN A 94 " pdb=" CB ASN A 94 " ideal model delta sigma weight residual 110.34 120.96 -10.62 1.30e+00 5.92e-01 6.67e+01 angle pdb=" C GLY C 509 " pdb=" N THR C 510 " pdb=" CA THR C 510 " ideal model delta sigma weight residual 120.23 108.94 11.29 1.67e+00 3.59e-01 4.57e+01 angle pdb=" N MET A 503 " pdb=" CA MET A 503 " pdb=" C MET A 503 " ideal model delta sigma weight residual 111.11 103.45 7.66 1.20e+00 6.94e-01 4.07e+01 angle pdb=" N THR K 28 " pdb=" CA THR K 28 " pdb=" C THR K 28 " ideal model delta sigma weight residual 114.64 105.20 9.44 1.52e+00 4.33e-01 3.86e+01 angle pdb=" N THR L 28 " pdb=" CA THR L 28 " pdb=" C THR L 28 " ideal model delta sigma weight residual 114.64 105.20 9.44 1.52e+00 4.33e-01 3.86e+01 ... (remaining 24683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 10195 23.00 - 45.99: 885 45.99 - 68.99: 157 68.99 - 91.98: 61 91.98 - 114.98: 61 Dihedral angle restraints: 11359 sinusoidal: 5079 harmonic: 6280 Sorted by residual: dihedral pdb=" CB CYS B 498 " pdb=" SG CYS B 498 " pdb=" SG CYS B 502 " pdb=" CB CYS B 502 " ideal model delta sinusoidal sigma weight residual 93.00 167.49 -74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS C 498 " pdb=" SG CYS C 498 " pdb=" SG CYS C 502 " pdb=" CB CYS C 502 " ideal model delta sinusoidal sigma weight residual 93.00 164.29 -71.29 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS A 498 " pdb=" SG CYS A 498 " pdb=" SG CYS A 502 " pdb=" CB CYS A 502 " ideal model delta sinusoidal sigma weight residual 93.00 162.66 -69.66 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 11356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.907: 2781 0.907 - 1.814: 0 1.814 - 2.722: 0 2.722 - 3.629: 0 3.629 - 4.536: 5 Chirality restraints: 2786 Sorted by residual: chirality pdb=" C1 MAN W 4 " pdb=" O6 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 -2.14 4.54 2.00e-02 2.50e+03 5.14e+04 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 1.73 -4.13 2.00e-02 2.50e+03 4.27e+04 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-02 2.50e+03 1.27e+03 ... (remaining 2783 not shown) Planarity restraints: 3126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " -0.360 2.00e-02 2.50e+03 3.07e-01 1.17e+03 pdb=" C7 NAG B 602 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.321 2.00e-02 2.50e+03 2.79e-01 9.70e+02 pdb=" C7 NAG B 601 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " -0.287 2.00e-02 2.50e+03 2.48e-01 7.72e+02 pdb=" C7 NAG A 602 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " 0.439 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.063 2.00e-02 2.50e+03 ... (remaining 3123 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.41: 13 1.41 - 2.28: 29 2.28 - 3.16: 13725 3.16 - 4.03: 46290 4.03 - 4.90: 87387 Warning: very small nonbonded interaction distances. Nonbonded interactions: 147444 Sorted by model distance: nonbonded pdb=" CE LYS A 301 " pdb=" CG1 ILE D 56 " model vdw 0.538 3.840 nonbonded pdb=" CE LYS B 301 " pdb=" CG1 ILE G 56 " model vdw 0.780 3.840 nonbonded pdb=" NZ LYS B 301 " pdb=" CB ILE G 56 " model vdw 0.918 3.550 nonbonded pdb=" NZ LYS A 301 " pdb=" CB ILE D 56 " model vdw 0.959 3.550 nonbonded pdb=" NZ LYS A 301 " pdb=" CA ILE D 56 " model vdw 1.079 3.550 ... (remaining 147439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) selection = (chain 'C' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' } 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=1.00 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.910 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 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 : 0.011 0.955 18247 Z= 1.042 Angle : 1.032 12.855 24847 Z= 0.581 Chirality : 0.188 4.536 2786 Planarity : 0.012 0.307 3114 Dihedral : 19.426 114.979 7278 Min Nonbonded Distance : 0.538 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 1.78 % Allowed : 24.41 % Favored : 73.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.25 % 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: -0.58 (0.18), residues: 2142 helix: 1.76 (0.27), residues: 345 sheet: -0.13 (0.23), residues: 528 loop : -1.15 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.052 0.002 TYR C 516 PHE 0.016 0.002 PHE I 71 TRP 0.022 0.001 TRP B 86 HIS 0.014 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.33 (18185) covalent geometry : angle 0.99176 / 0.57 (24688) SS BOND : bond 0.00493 / 0.29 ( 21) SS BOND : angle 2.46553 / 1.34 ( 42) hydrogen bonds : bond 0.16703 / 11.06 ( 627) hydrogen bonds : angle 7.62569 / 5.39 ( 1770) Misc. bond : bond 0.94288 / 47.38 ( 2) link_ALPHA1-3 : bond 0.00974 / 0.49 ( 3) link_ALPHA1-3 : angle 0.63054 / 0.40 ( 9) link_ALPHA1-6 : bond 0.00206 / 0.10 ( 3) link_ALPHA1-6 : angle 1.11231 / 0.78 ( 9) link_BETA1-2 : bond 0.00110 / 0.05 ( 3) link_BETA1-2 : angle 0.83274 / 0.51 ( 9) link_BETA1-4 : bond 0.01188 / 0.70 ( 15) link_BETA1-4 : angle 4.44744 / 3.06 ( 45) link_BETA2-3 : bond 0.00045 / 0.02 ( 3) link_BETA2-3 : angle 6.15194 / 3.72 ( 9) link_NAG-ASN : bond 0.00796 / 0.39 ( 12) link_NAG-ASN : angle 4.38987 / 2.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6944 (m-40) cc_final: 0.6706 (t0) REVERT: A 64 ASP cc_start: 0.6186 (p0) cc_final: 0.5746 (t0) REVERT: A 94 ASN cc_start: 0.7095 (OUTLIER) cc_final: 0.6886 (m-40) REVERT: A 157 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.6597 (mtm-85) REVERT: A 294 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6946 (mm-30) REVERT: A 331 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7599 (mtmm) REVERT: A 403 THR cc_start: 0.7253 (m) cc_final: 0.6920 (p) REVERT: A 423 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 426 ASN cc_start: 0.6661 (p0) cc_final: 0.6369 (t0) REVERT: A 456 MET cc_start: 0.6850 (mtt) cc_final: 0.6613 (mmp) REVERT: A 475 LYS cc_start: 0.7029 (ttpt) cc_final: 0.6688 (ttpp) REVERT: B 24 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6483 (mt-10) REVERT: B 31 GLU cc_start: 0.7274 (tt0) cc_final: 0.6629 (pt0) REVERT: B 64 ASP cc_start: 0.6823 (p0) cc_final: 0.6225 (t0) REVERT: B 114 MET cc_start: 0.6432 (ttp) cc_final: 0.6187 (ttp) REVERT: B 117 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6929 (mpt-90) REVERT: B 122 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7229 (mm-30) REVERT: B 157 ARG cc_start: 0.7359 (mtt-85) cc_final: 0.6688 (mtm-85) REVERT: B 248 LYS cc_start: 0.6695 (mmtt) cc_final: 0.6478 (mmpt) REVERT: B 256 GLU cc_start: 0.7684 (tt0) cc_final: 0.7292 (tt0) REVERT: B 325 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6459 (pt0) REVERT: B 328 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7154 (mmtt) REVERT: B 379 HIS cc_start: 0.8462 (t-170) cc_final: 0.8261 (OUTLIER) REVERT: B 403 THR cc_start: 0.7115 (m) cc_final: 0.6906 (p) REVERT: B 420 VAL cc_start: 0.6978 (p) cc_final: 0.6531 (m) REVERT: B 429 ARG cc_start: 0.6602 (mmt-90) cc_final: 0.6087 (mmp-170) REVERT: B 431 ILE cc_start: 0.6881 (mm) cc_final: 0.6592 (mp) REVERT: B 456 MET cc_start: 0.6922 (mtp) cc_final: 0.6539 (mtm) REVERT: B 475 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6646 (ttpp) REVERT: B 486 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 489 ASN cc_start: 0.7722 (p0) cc_final: 0.7517 (p0) REVERT: B 493 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7589 (tt0) REVERT: C 20 ASN cc_start: 0.7425 (m110) cc_final: 0.7152 (m-40) REVERT: C 63 LYS cc_start: 0.5647 (mtmt) cc_final: 0.5364 (mttm) REVERT: C 64 ASP cc_start: 0.6753 (p0) cc_final: 0.5902 (t0) REVERT: C 79 GLU cc_start: 0.7310 (tt0) cc_final: 0.7000 (mt-10) REVERT: C 157 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.6753 (mtm-85) REVERT: C 294 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 328 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7449 (mmmt) REVERT: C 331 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8013 (mtmm) REVERT: C 429 ARG cc_start: 0.6825 (mmp80) cc_final: 0.6608 (mmp-170) REVERT: C 433 ASN cc_start: 0.7650 (t0) cc_final: 0.7292 (t0) REVERT: C 456 MET cc_start: 0.7196 (mtt) cc_final: 0.6474 (mtm) REVERT: C 493 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7664 (tt0) REVERT: C 516 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: G 69 MET cc_start: 0.7931 (mtp) cc_final: 0.7690 (mtt) outliers start: 34 outliers final: 11 residues processed: 353 average time/residue: 0.5370 time to fit residues: 213.6102 Evaluate side-chains 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 HIS B 234 ASN B 425 ASN C 179 ASN C 333 ASN C 380 HIS C 404 ASN C 425 ASN H 58 ASN H 95 GLN L 22 ASN L 27 HIS D 58 ASN D 95 GLN I 22 ASN I 27 HIS G 95 GLN K 22 ASN K 27 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123991 restraints weight = 19101.999| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.96 r_work: 0.3155 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 18247 Z= 0.225 Angle : 0.818 19.119 24847 Z= 0.382 Chirality : 0.052 0.635 2786 Planarity : 0.005 0.054 3114 Dihedral : 11.728 93.389 3242 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 4.83 % Allowed : 21.57 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.46 (0.18), residues: 2142 helix: 1.78 (0.28), residues: 357 sheet: 0.07 (0.24), residues: 486 loop : -1.09 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.031 0.002 TYR K 27D PHE 0.016 0.002 PHE B 357 TRP 0.011 0.002 TRP C 70 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (18185) covalent geometry : angle 0.75780 / 0.37 (24688) SS BOND : bond 0.00544 / 0.32 ( 21) SS BOND : angle 1.38462 / 0.87 ( 42) hydrogen bonds : bond 0.04545 / 2.98 ( 627) hydrogen bonds : angle 5.78619 / 4.06 ( 1770) Misc. bond : bond 0.00733 / 0.36 ( 2) link_ALPHA1-3 : bond 0.00824 / 0.42 ( 3) link_ALPHA1-3 : angle 1.00471 / 0.61 ( 9) link_ALPHA1-6 : bond 0.00865 / 0.43 ( 3) link_ALPHA1-6 : angle 2.03044 / 1.25 ( 9) link_BETA1-2 : bond 0.00192 / 0.10 ( 3) link_BETA1-2 : angle 0.93728 / 0.53 ( 9) link_BETA1-4 : bond 0.00807 / 0.44 ( 15) link_BETA1-4 : angle 3.44165 / 2.15 ( 45) link_BETA2-3 : bond 0.01198 / 0.61 ( 3) link_BETA2-3 : angle 5.94513 / 3.35 ( 9) link_NAG-ASN : bond 0.00455 / 0.23 ( 12) link_NAG-ASN : angle 6.40544 / 4.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8357 (mt) REVERT: A 55 ASN cc_start: 0.9115 (t0) cc_final: 0.8915 (t0) REVERT: A 64 ASP cc_start: 0.7476 (p0) cc_final: 0.7192 (t0) REVERT: A 157 ARG cc_start: 0.8559 (mtt-85) cc_final: 0.8183 (mtm-85) REVERT: A 206 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8203 (tptt) REVERT: A 331 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8399 (mtmm) REVERT: A 420 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 423 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: A 456 MET cc_start: 0.7889 (mtt) cc_final: 0.7611 (mtm) REVERT: A 475 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7365 (ttpp) REVERT: B 63 LYS cc_start: 0.7320 (mttm) cc_final: 0.6944 (mtmm) REVERT: B 64 ASP cc_start: 0.7670 (p0) cc_final: 0.7224 (t0) REVERT: B 122 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8478 (mt-10) REVERT: B 157 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8267 (mtm-85) REVERT: B 328 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8297 (mmtt) REVERT: B 342 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7680 (ptp-170) REVERT: B 456 MET cc_start: 0.7840 (mtp) cc_final: 0.7530 (mtm) REVERT: B 475 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7455 (ttpp) REVERT: B 486 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 489 ASN cc_start: 0.8069 (p0) cc_final: 0.7825 (p0) REVERT: C 20 ASN cc_start: 0.7902 (m110) cc_final: 0.7449 (m-40) REVERT: C 25 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: C 63 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7071 (mttp) REVERT: C 64 ASP cc_start: 0.7697 (p0) cc_final: 0.7107 (t0) REVERT: C 157 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8226 (mtm-85) REVERT: C 313 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: C 328 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8539 (mmmt) REVERT: C 331 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8759 (mtmm) REVERT: C 409 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7775 (mp) REVERT: C 456 MET cc_start: 0.7969 (mtt) cc_final: 0.7618 (mtm) REVERT: C 459 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: C 485 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7070 (ttmm) REVERT: C 493 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7544 (tt0) REVERT: C 521 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.5729 (ttp80) REVERT: L 58 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7909 (m) REVERT: I 58 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8035 (m) REVERT: I 60 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7057 (t0) REVERT: G 79 SER cc_start: 0.8485 (m) cc_final: 0.8194 (t) REVERT: K 4 MET cc_start: 0.9014 (mmm) cc_final: 0.8773 (mmm) REVERT: K 105 GLU cc_start: 0.5159 (tm-30) cc_final: 0.4782 (mt-10) outliers start: 92 outliers final: 30 residues processed: 289 average time/residue: 0.6013 time to fit residues: 194.5766 Evaluate side-chains 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 521 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain K residue 27 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 74 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 425 ASN C 333 ASN L 22 ASN I 22 ASN I 90 GLN K 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125022 restraints weight = 19251.930| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.00 r_work: 0.3196 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18247 Z= 0.135 Angle : 0.679 15.851 24847 Z= 0.319 Chirality : 0.048 0.617 2786 Planarity : 0.004 0.056 3114 Dihedral : 9.861 89.927 3229 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 3.73 % Allowed : 22.15 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.22 (0.18), residues: 2142 helix: 2.04 (0.28), residues: 357 sheet: 0.17 (0.23), residues: 534 loop : -0.97 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 105 TYR 0.023 0.002 TYR K 27D PHE 0.012 0.002 PHE I 27C TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18185) covalent geometry : angle 0.62830 / 0.31 (24688) SS BOND : bond 0.00285 / 0.18 ( 21) SS BOND : angle 1.16157 / 0.70 ( 42) hydrogen bonds : bond 0.03959 / 2.58 ( 627) hydrogen bonds : angle 5.34802 / 3.75 ( 1770) Misc. bond : bond 0.00582 / 0.31 ( 2) link_ALPHA1-3 : bond 0.00841 / 0.42 ( 3) link_ALPHA1-3 : angle 0.92525 / 0.57 ( 9) link_ALPHA1-6 : bond 0.01095 / 0.54 ( 3) link_ALPHA1-6 : angle 2.00771 / 1.21 ( 9) link_BETA1-2 : bond 0.00132 / 0.07 ( 3) link_BETA1-2 : angle 0.94271 / 0.56 ( 9) link_BETA1-4 : bond 0.00673 / 0.36 ( 15) link_BETA1-4 : angle 3.25674 / 2.08 ( 45) link_BETA2-3 : bond 0.01056 / 0.53 ( 3) link_BETA2-3 : angle 5.29469 / 2.91 ( 9) link_NAG-ASN : bond 0.00850 / 0.55 ( 12) link_NAG-ASN : angle 4.96364 / 3.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A 64 ASP cc_start: 0.7621 (p0) cc_final: 0.7395 (t0) REVERT: A 157 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8337 (mtm-85) REVERT: A 331 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8488 (mtmm) REVERT: A 403 THR cc_start: 0.7864 (m) cc_final: 0.7550 (p) REVERT: A 423 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: A 456 MET cc_start: 0.7905 (mtt) cc_final: 0.7673 (mtm) REVERT: A 475 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7544 (ttpp) REVERT: B 63 LYS cc_start: 0.7402 (mttm) cc_final: 0.7065 (mtmm) REVERT: B 64 ASP cc_start: 0.7711 (p0) cc_final: 0.7364 (t0) REVERT: B 157 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.8362 (mtm-85) REVERT: B 175 LYS cc_start: 0.8751 (mtpm) cc_final: 0.8527 (mtmp) REVERT: B 328 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8452 (mmtt) REVERT: B 342 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7764 (ptp-170) REVERT: B 420 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 456 MET cc_start: 0.7911 (mtp) cc_final: 0.7631 (mtm) REVERT: B 475 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7639 (ttpp) REVERT: B 486 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 489 ASN cc_start: 0.8197 (p0) cc_final: 0.7943 (p0) REVERT: C 20 ASN cc_start: 0.7853 (m110) cc_final: 0.7555 (m-40) REVERT: C 63 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7273 (mttp) REVERT: C 64 ASP cc_start: 0.7772 (p0) cc_final: 0.7270 (t0) REVERT: C 157 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8328 (mtm-85) REVERT: C 409 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 456 MET cc_start: 0.8029 (mtt) cc_final: 0.7711 (mtm) REVERT: C 459 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: C 485 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7370 (ttmm) REVERT: C 493 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7697 (tt0) REVERT: H 3 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7450 (mptt) REVERT: H 79 SER cc_start: 0.8569 (m) cc_final: 0.8317 (t) REVERT: L 105 GLU cc_start: 0.5524 (tm-30) cc_final: 0.5060 (mt-10) REVERT: D 3 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7454 (mptt) REVERT: D 79 SER cc_start: 0.8637 (m) cc_final: 0.8333 (t) REVERT: I 105 GLU cc_start: 0.5319 (tm-30) cc_final: 0.4890 (mt-10) REVERT: G 3 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7451 (mptt) REVERT: G 38 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7923 (ptt180) REVERT: G 79 SER cc_start: 0.8524 (m) cc_final: 0.8276 (t) REVERT: K 105 GLU cc_start: 0.5449 (tm-30) cc_final: 0.5053 (mt-10) outliers start: 71 outliers final: 29 residues processed: 267 average time/residue: 0.5715 time to fit residues: 171.9542 Evaluate side-chains 230 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 20 ASN C 333 ASN C 425 ASN H 58 ASN L 22 ASN I 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119401 restraints weight = 19168.640| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.98 r_work: 0.3182 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 18247 Z= 0.290 Angle : 0.801 15.420 24847 Z= 0.383 Chirality : 0.053 0.636 2786 Planarity : 0.005 0.059 3114 Dihedral : 9.128 83.752 3225 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 4.99 % Allowed : 21.73 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.50 (0.17), residues: 2142 helix: 1.83 (0.28), residues: 357 sheet: -0.09 (0.22), residues: 519 loop : -1.11 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 429 TYR 0.036 0.003 TYR I 27D PHE 0.018 0.002 PHE B 357 TRP 0.012 0.002 TRP G 47 HIS 0.007 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (18185) covalent geometry : angle 0.75063 / 0.37 (24688) SS BOND : bond 0.00471 / 0.28 ( 21) SS BOND : angle 1.46837 / 0.97 ( 42) hydrogen bonds : bond 0.04654 / 3.06 ( 627) hydrogen bonds : angle 5.50570 / 3.86 ( 1770) Misc. bond : bond 0.00807 / 0.41 ( 2) link_ALPHA1-3 : bond 0.00855 / 0.43 ( 3) link_ALPHA1-3 : angle 1.03602 / 0.55 ( 9) link_ALPHA1-6 : bond 0.01093 / 0.54 ( 3) link_ALPHA1-6 : angle 1.87142 / 1.19 ( 9) link_BETA1-2 : bond 0.00350 / 0.17 ( 3) link_BETA1-2 : angle 1.27804 / 0.65 ( 9) link_BETA1-4 : bond 0.00665 / 0.36 ( 15) link_BETA1-4 : angle 3.49695 / 2.20 ( 45) link_BETA2-3 : bond 0.00923 / 0.45 ( 3) link_BETA2-3 : angle 6.87483 / 3.92 ( 9) link_NAG-ASN : bond 0.00817 / 0.51 ( 12) link_NAG-ASN : angle 5.00618 / 3.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 202 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 117 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7379 (mpt-90) REVERT: A 157 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8394 (mtm-85) REVERT: A 423 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: A 456 MET cc_start: 0.8097 (mtt) cc_final: 0.7829 (mtm) REVERT: B 63 LYS cc_start: 0.7564 (mttm) cc_final: 0.7206 (mtmm) REVERT: B 64 ASP cc_start: 0.7884 (p0) cc_final: 0.7503 (t0) REVERT: B 157 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8413 (mtm-85) REVERT: B 184 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: B 186 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 328 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8395 (mmtt) REVERT: B 342 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: B 356 LEU cc_start: 0.8287 (mt) cc_final: 0.8076 (mt) REVERT: B 456 MET cc_start: 0.7920 (mtp) cc_final: 0.7692 (mtm) REVERT: B 486 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 489 ASN cc_start: 0.8309 (p0) cc_final: 0.8061 (p0) REVERT: C 20 ASN cc_start: 0.7971 (m-40) cc_final: 0.7685 (m-40) REVERT: C 63 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7415 (mttp) REVERT: C 64 ASP cc_start: 0.7793 (p0) cc_final: 0.7314 (m-30) REVERT: C 117 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7384 (mpt-90) REVERT: C 157 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8412 (mtm-85) REVERT: C 248 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8408 (mptm) REVERT: C 409 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 456 MET cc_start: 0.8098 (mtt) cc_final: 0.7844 (mtm) REVERT: C 459 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: C 485 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7444 (ttmm) REVERT: C 493 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7753 (tt0) REVERT: H 4 LEU cc_start: 0.8275 (mm) cc_final: 0.7948 (mt) REVERT: H 81 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7864 (tppp) REVERT: H 105 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7256 (mpp-170) REVERT: L 105 GLU cc_start: 0.5678 (tm-30) cc_final: 0.5214 (mt-10) REVERT: D 3 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7478 (mptt) REVERT: D 77 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6794 (mp) REVERT: I 4 MET cc_start: 0.9015 (mmm) cc_final: 0.8400 (mmm) REVERT: I 105 GLU cc_start: 0.5510 (tm-30) cc_final: 0.5030 (mt-10) REVERT: G 3 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7408 (mptt) REVERT: G 79 SER cc_start: 0.8547 (m) cc_final: 0.8257 (t) REVERT: K 58 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8201 (m) REVERT: K 105 GLU cc_start: 0.5626 (tm-30) cc_final: 0.5176 (mt-10) outliers start: 95 outliers final: 44 residues processed: 274 average time/residue: 0.5633 time to fit residues: 174.1435 Evaluate side-chains 249 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 90 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 333 ASN L 22 ASN I 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126540 restraints weight = 18817.036| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.73 r_work: 0.3232 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18247 Z= 0.123 Angle : 0.656 15.092 24847 Z= 0.310 Chirality : 0.047 0.545 2786 Planarity : 0.004 0.051 3114 Dihedral : 8.538 88.721 3225 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 4.41 % Allowed : 22.89 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.22 (0.18), residues: 2142 helix: 2.13 (0.28), residues: 357 sheet: 0.12 (0.23), residues: 531 loop : -0.97 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.050 0.002 TYR K 27D PHE 0.017 0.001 PHE K 27C TRP 0.013 0.001 TRP C 446 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (18185) covalent geometry : angle 0.60627 / 0.30 (24688) SS BOND : bond 0.00258 / 0.16 ( 21) SS BOND : angle 1.15998 / 0.66 ( 42) hydrogen bonds : bond 0.03745 / 2.44 ( 627) hydrogen bonds : angle 5.10951 / 3.58 ( 1770) Misc. bond : bond 0.01897 / 0.91 ( 2) link_ALPHA1-3 : bond 0.00876 / 0.44 ( 3) link_ALPHA1-3 : angle 0.90256 / 0.56 ( 9) link_ALPHA1-6 : bond 0.01039 / 0.51 ( 3) link_ALPHA1-6 : angle 1.67249 / 1.01 ( 9) link_BETA1-2 : bond 0.00090 / 0.05 ( 3) link_BETA1-2 : angle 1.03890 / 0.62 ( 9) link_BETA1-4 : bond 0.00647 / 0.35 ( 15) link_BETA1-4 : angle 3.22811 / 2.05 ( 45) link_BETA2-3 : bond 0.00560 / 0.28 ( 3) link_BETA2-3 : angle 5.53609 / 2.99 ( 9) link_NAG-ASN : bond 0.00791 / 0.50 ( 12) link_NAG-ASN : angle 4.60068 / 3.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 157 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8314 (mtm-85) REVERT: A 160 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8599 (t) REVERT: A 240 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: A 423 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 456 MET cc_start: 0.7932 (mtt) cc_final: 0.7688 (mtm) REVERT: B 61 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8830 (mt) REVERT: B 63 LYS cc_start: 0.7427 (mttm) cc_final: 0.7083 (mtmm) REVERT: B 64 ASP cc_start: 0.7805 (p0) cc_final: 0.7478 (t0) REVERT: B 81 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (mp) REVERT: B 117 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7343 (mpt-90) REVERT: B 157 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8394 (mtm-85) REVERT: B 160 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (t) REVERT: B 175 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8504 (mtmp) REVERT: B 328 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8434 (mmtt) REVERT: B 342 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7785 (ptp-170) REVERT: B 456 MET cc_start: 0.7816 (mtp) cc_final: 0.7604 (mtm) REVERT: B 486 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 489 ASN cc_start: 0.8208 (p0) cc_final: 0.7951 (p0) REVERT: C 20 ASN cc_start: 0.7791 (m-40) cc_final: 0.7447 (m-40) REVERT: C 25 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: C 63 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7282 (mptp) REVERT: C 64 ASP cc_start: 0.7839 (p0) cc_final: 0.7419 (m-30) REVERT: C 157 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8365 (mtm-85) REVERT: C 294 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: C 313 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7872 (mtt) REVERT: C 409 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (mm) REVERT: C 456 MET cc_start: 0.7981 (mtt) cc_final: 0.7711 (mtm) REVERT: C 459 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: C 485 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7522 (ttmm) REVERT: H 3 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7294 (mptt) REVERT: H 66 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7736 (ptm-80) REVERT: L 105 GLU cc_start: 0.5701 (tm-30) cc_final: 0.5274 (mt-10) REVERT: D 3 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7296 (mptt) REVERT: I 4 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: I 105 GLU cc_start: 0.5453 (tm-30) cc_final: 0.5074 (mt-10) REVERT: G 3 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7191 (mptt) REVERT: G 38 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7893 (ptt180) REVERT: G 79 SER cc_start: 0.8529 (m) cc_final: 0.8285 (t) REVERT: K 4 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8513 (mmm) REVERT: K 105 GLU cc_start: 0.5591 (tm-30) cc_final: 0.5204 (mt-10) outliers start: 84 outliers final: 29 residues processed: 272 average time/residue: 0.5500 time to fit residues: 168.9314 Evaluate side-chains 244 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain K residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 64 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 153 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 212 optimal weight: 0.0040 overall best weight: 1.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 425 ASN C 425 ASN L 22 ASN I 22 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120758 restraints weight = 19059.185| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.90 r_work: 0.3222 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18247 Z= 0.202 Angle : 0.691 13.843 24847 Z= 0.331 Chirality : 0.049 0.570 2786 Planarity : 0.005 0.052 3114 Dihedral : 8.282 86.976 3225 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.99 % Allowed : 23.78 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.31 (0.18), residues: 2142 helix: 2.06 (0.28), residues: 357 sheet: 0.00 (0.23), residues: 516 loop : -0.99 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.044 0.002 TYR K 27D PHE 0.015 0.002 PHE I 91 TRP 0.012 0.001 TRP G 47 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (18185) covalent geometry : angle 0.64196 / 0.32 (24688) SS BOND : bond 0.00574 / 0.32 ( 21) SS BOND : angle 1.31806 / 0.82 ( 42) hydrogen bonds : bond 0.04109 / 2.69 ( 627) hydrogen bonds : angle 5.14117 / 3.60 ( 1770) Misc. bond : bond 0.01491 / 0.74 ( 2) link_ALPHA1-3 : bond 0.00857 / 0.43 ( 3) link_ALPHA1-3 : angle 0.98919 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00906 / 0.45 ( 3) link_ALPHA1-6 : angle 1.52480 / 0.93 ( 9) link_BETA1-2 : bond 0.00211 / 0.11 ( 3) link_BETA1-2 : angle 1.11348 / 0.60 ( 9) link_BETA1-4 : bond 0.00642 / 0.35 ( 15) link_BETA1-4 : angle 3.28542 / 2.08 ( 45) link_BETA2-3 : bond 0.00665 / 0.34 ( 3) link_BETA2-3 : angle 6.10165 / 3.38 ( 9) link_NAG-ASN : bond 0.00776 / 0.48 ( 12) link_NAG-ASN : angle 4.52989 / 3.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 157 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8318 (mtm-85) REVERT: A 240 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9116 (mtt) REVERT: A 313 MET cc_start: 0.8601 (mtt) cc_final: 0.8008 (mtt) REVERT: A 423 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: A 456 MET cc_start: 0.8018 (mtt) cc_final: 0.7754 (mtm) REVERT: B 63 LYS cc_start: 0.7471 (mttm) cc_final: 0.7122 (mtmm) REVERT: B 64 ASP cc_start: 0.7790 (p0) cc_final: 0.7426 (t0) REVERT: B 81 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 117 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7422 (mpt-90) REVERT: B 157 ARG cc_start: 0.8637 (mtt-85) cc_final: 0.8352 (mtm-85) REVERT: B 175 LYS cc_start: 0.8781 (mtpm) cc_final: 0.8480 (mtmp) REVERT: B 186 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8620 (mp) REVERT: B 328 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8401 (mmtt) REVERT: B 342 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7815 (ptp-170) REVERT: B 456 MET cc_start: 0.7828 (mtp) cc_final: 0.7614 (mtm) REVERT: B 486 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 489 ASN cc_start: 0.8177 (p0) cc_final: 0.7941 (p0) REVERT: C 20 ASN cc_start: 0.7786 (m-40) cc_final: 0.7423 (m-40) REVERT: C 25 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: C 63 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7339 (mttp) REVERT: C 64 ASP cc_start: 0.7813 (p0) cc_final: 0.7395 (m-30) REVERT: C 157 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.8358 (mtm-85) REVERT: C 294 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: C 313 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: C 409 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 456 MET cc_start: 0.8001 (mtt) cc_final: 0.7736 (mtm) REVERT: C 459 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: C 485 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7464 (ttmm) REVERT: H 105 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7131 (mpp-170) REVERT: L 105 GLU cc_start: 0.5671 (tm-30) cc_final: 0.5275 (mt-10) REVERT: D 3 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7174 (mptt) REVERT: I 4 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: I 105 GLU cc_start: 0.5566 (tm-30) cc_final: 0.5006 (mt-10) REVERT: G 3 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7227 (mptt) REVERT: G 20 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7587 (mm) REVERT: G 38 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7792 (ptt180) REVERT: G 79 SER cc_start: 0.8549 (m) cc_final: 0.8278 (t) REVERT: K 105 GLU cc_start: 0.5655 (tm-30) cc_final: 0.5258 (mt-10) outliers start: 76 outliers final: 36 residues processed: 256 average time/residue: 0.5525 time to fit residues: 159.8213 Evaluate side-chains 240 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN L 22 ASN I 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121071 restraints weight = 19233.746| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.94 r_work: 0.3218 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 18247 Z= 0.193 Angle : 0.687 18.686 24847 Z= 0.330 Chirality : 0.048 0.550 2786 Planarity : 0.004 0.051 3114 Dihedral : 8.119 86.064 3225 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 4.46 % Allowed : 23.36 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.29 (0.18), residues: 2142 helix: 2.07 (0.28), residues: 357 sheet: -0.03 (0.23), residues: 519 loop : -0.96 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 429 TYR 0.055 0.002 TYR K 27D PHE 0.014 0.002 PHE K 91 TRP 0.014 0.001 TRP C 375 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (18185) covalent geometry : angle 0.64046 / 0.32 (24688) SS BOND : bond 0.00340 / 0.20 ( 21) SS BOND : angle 1.30372 / 0.79 ( 42) hydrogen bonds : bond 0.04036 / 2.64 ( 627) hydrogen bonds : angle 5.10347 / 3.57 ( 1770) Misc. bond : bond 0.01209 / 0.58 ( 2) link_ALPHA1-3 : bond 0.00862 / 0.43 ( 3) link_ALPHA1-3 : angle 0.99175 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00830 / 0.41 ( 3) link_ALPHA1-6 : angle 1.47976 / 0.89 ( 9) link_BETA1-2 : bond 0.00178 / 0.09 ( 3) link_BETA1-2 : angle 1.11593 / 0.62 ( 9) link_BETA1-4 : bond 0.00639 / 0.34 ( 15) link_BETA1-4 : angle 3.27040 / 2.07 ( 45) link_BETA2-3 : bond 0.00711 / 0.36 ( 3) link_BETA2-3 : angle 6.03626 / 3.32 ( 9) link_NAG-ASN : bond 0.00735 / 0.45 ( 12) link_NAG-ASN : angle 4.32258 / 2.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 117 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7188 (mpt-90) REVERT: A 157 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8339 (mtm-85) REVERT: A 423 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: A 456 MET cc_start: 0.8036 (mtt) cc_final: 0.7779 (mtm) REVERT: B 63 LYS cc_start: 0.7510 (mttm) cc_final: 0.7152 (mtmm) REVERT: B 64 ASP cc_start: 0.7806 (p0) cc_final: 0.7449 (t0) REVERT: B 81 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 117 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7471 (mpt-90) REVERT: B 157 ARG cc_start: 0.8643 (mtt-85) cc_final: 0.8357 (mtm-85) REVERT: B 175 LYS cc_start: 0.8766 (mtpm) cc_final: 0.8472 (mtmp) REVERT: B 186 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 328 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8406 (mmtt) REVERT: B 342 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7903 (ptp-170) REVERT: B 456 MET cc_start: 0.7839 (mtp) cc_final: 0.7618 (mtm) REVERT: B 486 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 489 ASN cc_start: 0.8211 (p0) cc_final: 0.7974 (p0) REVERT: C 20 ASN cc_start: 0.7726 (m-40) cc_final: 0.7395 (m-40) REVERT: C 25 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: C 63 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7371 (mttp) REVERT: C 64 ASP cc_start: 0.7814 (p0) cc_final: 0.7420 (m-30) REVERT: C 117 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7249 (mpt-90) REVERT: C 157 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8366 (mtm-85) REVERT: C 294 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: C 313 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: C 409 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 456 MET cc_start: 0.8009 (mtt) cc_final: 0.7748 (mtm) REVERT: C 459 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 485 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7475 (ttmm) REVERT: H 105 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7227 (mpp-170) REVERT: L 4 MET cc_start: 0.9024 (mmm) cc_final: 0.8611 (mmm) REVERT: L 105 GLU cc_start: 0.5629 (tm-30) cc_final: 0.5283 (mt-10) REVERT: D 3 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7178 (mptt) REVERT: I 4 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: I 58 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8114 (m) REVERT: I 105 GLU cc_start: 0.5584 (tm-30) cc_final: 0.5030 (mt-10) REVERT: G 3 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7175 (mptt) REVERT: G 38 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7817 (ptt180) REVERT: G 66 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7529 (mtm-85) REVERT: K 4 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (mmm) REVERT: K 105 GLU cc_start: 0.5601 (tm-30) cc_final: 0.5257 (mt-10) outliers start: 85 outliers final: 38 residues processed: 263 average time/residue: 0.5704 time to fit residues: 168.8377 Evaluate side-chains 253 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain K residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 120 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 425 ASN L 22 ASN I 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122751 restraints weight = 18796.018| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.74 r_work: 0.3234 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 18247 Z= 0.195 Angle : 0.720 23.714 24847 Z= 0.341 Chirality : 0.048 0.546 2786 Planarity : 0.004 0.051 3114 Dihedral : 8.041 85.558 3225 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 4.41 % Allowed : 23.52 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.31 (0.18), residues: 2142 helix: 2.06 (0.28), residues: 357 sheet: -0.04 (0.23), residues: 519 loop : -0.96 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 105 TYR 0.034 0.002 TYR I 27D PHE 0.013 0.002 PHE I 27C TRP 0.018 0.001 TRP C 375 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (18185) covalent geometry : angle 0.67662 / 0.33 (24688) SS BOND : bond 0.00363 / 0.21 ( 21) SS BOND : angle 1.35519 / 0.83 ( 42) hydrogen bonds : bond 0.04063 / 2.66 ( 627) hydrogen bonds : angle 5.10154 / 3.57 ( 1770) Misc. bond : bond 0.00800 / 0.41 ( 2) link_ALPHA1-3 : bond 0.00872 / 0.44 ( 3) link_ALPHA1-3 : angle 1.01542 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00766 / 0.38 ( 3) link_ALPHA1-6 : angle 1.47258 / 0.89 ( 9) link_BETA1-2 : bond 0.00183 / 0.09 ( 3) link_BETA1-2 : angle 1.14325 / 0.63 ( 9) link_BETA1-4 : bond 0.00634 / 0.34 ( 15) link_BETA1-4 : angle 3.27853 / 2.07 ( 45) link_BETA2-3 : bond 0.00634 / 0.32 ( 3) link_BETA2-3 : angle 6.07941 / 3.35 ( 9) link_NAG-ASN : bond 0.00734 / 0.45 ( 12) link_NAG-ASN : angle 4.23402 / 2.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 196 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 117 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7219 (mpt-90) REVERT: A 157 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8345 (mtm-85) REVERT: A 423 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: A 456 MET cc_start: 0.7996 (mtt) cc_final: 0.7739 (mtm) REVERT: B 63 LYS cc_start: 0.7491 (mttm) cc_final: 0.7138 (mtmm) REVERT: B 64 ASP cc_start: 0.7771 (p0) cc_final: 0.7465 (t0) REVERT: B 81 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8097 (mp) REVERT: B 117 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7423 (mpt-90) REVERT: B 157 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8342 (mtm-85) REVERT: B 175 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8455 (mtmp) REVERT: B 186 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 328 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8378 (mmtt) REVERT: B 342 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: B 413 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7089 (mpp) REVERT: B 423 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: B 431 ILE cc_start: 0.8862 (mm) cc_final: 0.8539 (mp) REVERT: B 456 MET cc_start: 0.7799 (mtp) cc_final: 0.7576 (mtm) REVERT: B 486 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 489 ASN cc_start: 0.8246 (p0) cc_final: 0.8025 (p0) REVERT: C 20 ASN cc_start: 0.7719 (m-40) cc_final: 0.7368 (m-40) REVERT: C 25 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: C 63 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7408 (mttp) REVERT: C 64 ASP cc_start: 0.7796 (p0) cc_final: 0.7429 (m-30) REVERT: C 117 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7248 (mpt-90) REVERT: C 157 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8365 (mtm-85) REVERT: C 290 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8449 (mmtm) REVERT: C 294 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: C 313 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: C 409 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 411 ASP cc_start: 0.7166 (t0) cc_final: 0.6895 (m-30) REVERT: C 456 MET cc_start: 0.8012 (mtt) cc_final: 0.7755 (mtm) REVERT: C 459 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 485 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7531 (ttmm) REVERT: H 105 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7221 (mpp-170) REVERT: L 105 GLU cc_start: 0.5701 (tm-30) cc_final: 0.5380 (mt-10) REVERT: I 4 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: I 58 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8128 (m) REVERT: I 105 GLU cc_start: 0.5579 (tm-30) cc_final: 0.5004 (mt-10) REVERT: G 38 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7795 (ptt180) REVERT: G 66 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7552 (mtm-85) REVERT: K 4 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8550 (mmm) REVERT: K 105 GLU cc_start: 0.5621 (tm-30) cc_final: 0.5337 (mt-10) outliers start: 84 outliers final: 42 residues processed: 261 average time/residue: 0.5574 time to fit residues: 163.7537 Evaluate side-chains 257 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 192 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain K residue 4 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 102 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 379 HIS I 22 ASN K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120465 restraints weight = 19089.360| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.83 r_work: 0.3189 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 18247 Z= 0.228 Angle : 0.762 26.514 24847 Z= 0.360 Chirality : 0.050 0.550 2786 Planarity : 0.005 0.050 3114 Dihedral : 8.042 83.222 3225 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 4.15 % Allowed : 23.73 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.35 (0.18), residues: 2142 helix: 1.99 (0.27), residues: 357 sheet: -0.04 (0.23), residues: 519 loop : -0.99 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 429 TYR 0.028 0.002 TYR K 27D PHE 0.017 0.002 PHE I 27C TRP 0.021 0.002 TRP C 375 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (18185) covalent geometry : angle 0.72027 / 0.35 (24688) SS BOND : bond 0.00401 / 0.23 ( 21) SS BOND : angle 1.44492 / 0.92 ( 42) hydrogen bonds : bond 0.04232 / 2.78 ( 627) hydrogen bonds : angle 5.16402 / 3.61 ( 1770) Misc. bond : bond 0.00698 / 0.35 ( 2) link_ALPHA1-3 : bond 0.00883 / 0.44 ( 3) link_ALPHA1-3 : angle 1.08557 / 0.57 ( 9) link_ALPHA1-6 : bond 0.00731 / 0.37 ( 3) link_ALPHA1-6 : angle 1.46145 / 0.89 ( 9) link_BETA1-2 : bond 0.00197 / 0.10 ( 3) link_BETA1-2 : angle 1.23075 / 0.66 ( 9) link_BETA1-4 : bond 0.00627 / 0.34 ( 15) link_BETA1-4 : angle 3.32333 / 2.10 ( 45) link_BETA2-3 : bond 0.00673 / 0.34 ( 3) link_BETA2-3 : angle 6.31661 / 3.52 ( 9) link_NAG-ASN : bond 0.00726 / 0.45 ( 12) link_NAG-ASN : angle 4.19128 / 2.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 191 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 117 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7192 (mpt-90) REVERT: A 157 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8314 (mtm-85) REVERT: A 328 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8407 (mmmt) REVERT: A 423 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 456 MET cc_start: 0.7935 (mtt) cc_final: 0.7717 (mtm) REVERT: B 63 LYS cc_start: 0.7510 (mttm) cc_final: 0.7116 (mtmm) REVERT: B 64 ASP cc_start: 0.7764 (p0) cc_final: 0.7375 (t0) REVERT: B 81 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 117 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7442 (mpt-90) REVERT: B 157 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8288 (mtm-85) REVERT: B 175 LYS cc_start: 0.8754 (mtpm) cc_final: 0.8437 (mtmp) REVERT: B 186 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 328 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8317 (mmtt) REVERT: B 342 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7952 (ptp-170) REVERT: B 413 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: B 423 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: B 431 ILE cc_start: 0.8888 (mm) cc_final: 0.8565 (mp) REVERT: B 456 MET cc_start: 0.7802 (mtp) cc_final: 0.7572 (mtm) REVERT: B 486 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 489 ASN cc_start: 0.8229 (p0) cc_final: 0.7966 (p0) REVERT: C 20 ASN cc_start: 0.7748 (m-40) cc_final: 0.7418 (m-40) REVERT: C 25 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: C 63 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7374 (mttp) REVERT: C 64 ASP cc_start: 0.7792 (p0) cc_final: 0.7366 (m-30) REVERT: C 117 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7273 (mpt-90) REVERT: C 157 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8309 (mtm-85) REVERT: C 290 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8441 (mmtm) REVERT: C 294 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: C 313 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7819 (mtt) REVERT: C 409 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8095 (mm) REVERT: C 456 MET cc_start: 0.8001 (mtt) cc_final: 0.7725 (mtm) REVERT: C 459 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: C 485 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7464 (ttmm) REVERT: H 105 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7319 (mpp-170) REVERT: L 4 MET cc_start: 0.9042 (mmm) cc_final: 0.8749 (mmm) REVERT: L 105 GLU cc_start: 0.5667 (tm-30) cc_final: 0.5313 (mt-10) REVERT: I 4 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8331 (mmm) REVERT: I 105 GLU cc_start: 0.5577 (tm-30) cc_final: 0.5023 (mt-10) REVERT: G 38 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7816 (ptt180) REVERT: G 66 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7499 (mtm-85) REVERT: K 105 GLU cc_start: 0.5601 (tm-30) cc_final: 0.5283 (mt-10) outliers start: 79 outliers final: 41 residues processed: 251 average time/residue: 0.5242 time to fit residues: 147.9720 Evaluate side-chains 246 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 61 optimal weight: 0.0010 chunk 169 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 192 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125748 restraints weight = 18710.247| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.69 r_work: 0.3279 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18247 Z= 0.115 Angle : 0.674 26.371 24847 Z= 0.319 Chirality : 0.046 0.486 2786 Planarity : 0.004 0.049 3114 Dihedral : 7.855 87.966 3225 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.83 % Allowed : 25.20 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.14 (0.18), residues: 2142 helix: 2.21 (0.27), residues: 357 sheet: 0.11 (0.23), residues: 531 loop : -0.89 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 105 TYR 0.031 0.002 TYR I 27D PHE 0.016 0.001 PHE K 27C TRP 0.024 0.001 TRP C 375 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (18185) covalent geometry : angle 0.63261 / 0.31 (24688) SS BOND : bond 0.00294 / 0.18 ( 21) SS BOND : angle 1.20094 / 0.67 ( 42) hydrogen bonds : bond 0.03608 / 2.35 ( 627) hydrogen bonds : angle 4.92198 / 3.44 ( 1770) Misc. bond : bond 0.00660 / 0.35 ( 2) link_ALPHA1-3 : bond 0.00924 / 0.46 ( 3) link_ALPHA1-3 : angle 0.89252 / 0.53 ( 9) link_ALPHA1-6 : bond 0.00728 / 0.37 ( 3) link_ALPHA1-6 : angle 1.50041 / 0.89 ( 9) link_BETA1-2 : bond 0.00099 / 0.05 ( 3) link_BETA1-2 : angle 1.05228 / 0.61 ( 9) link_BETA1-4 : bond 0.00638 / 0.34 ( 15) link_BETA1-4 : angle 3.17545 / 2.01 ( 45) link_BETA2-3 : bond 0.00484 / 0.24 ( 3) link_BETA2-3 : angle 5.49570 / 2.93 ( 9) link_NAG-ASN : bond 0.00720 / 0.44 ( 12) link_NAG-ASN : angle 4.00236 / 2.64 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8338 (mt) REVERT: A 157 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8340 (mtm-85) REVERT: A 311 SER cc_start: 0.8906 (t) cc_final: 0.8677 (t) REVERT: A 423 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: A 456 MET cc_start: 0.7932 (mtt) cc_final: 0.7673 (mtm) REVERT: B 63 LYS cc_start: 0.7468 (mttm) cc_final: 0.7105 (mtmm) REVERT: B 64 ASP cc_start: 0.7672 (p0) cc_final: 0.7420 (t0) REVERT: B 117 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7256 (mpt-90) REVERT: B 157 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8318 (mtm-85) REVERT: B 175 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8444 (mtmp) REVERT: B 186 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8791 (mp) REVERT: B 328 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8416 (mmtt) REVERT: B 342 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7743 (ptp-170) REVERT: B 423 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: B 431 ILE cc_start: 0.8746 (mm) cc_final: 0.8418 (mp) REVERT: B 456 MET cc_start: 0.7746 (mtp) cc_final: 0.7518 (mtm) REVERT: B 486 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 489 ASN cc_start: 0.8285 (p0) cc_final: 0.7996 (p0) REVERT: C 25 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: C 63 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7427 (mttp) REVERT: C 64 ASP cc_start: 0.7822 (p0) cc_final: 0.7506 (m-30) REVERT: C 157 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8356 (mtm180) REVERT: C 411 ASP cc_start: 0.7130 (t0) cc_final: 0.6896 (m-30) REVERT: C 456 MET cc_start: 0.7981 (mtt) cc_final: 0.7730 (mtm) REVERT: C 459 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 489 ASN cc_start: 0.8030 (p0) cc_final: 0.7674 (p0) REVERT: L 4 MET cc_start: 0.8921 (mmm) cc_final: 0.8606 (mmm) REVERT: L 105 GLU cc_start: 0.5693 (tm-30) cc_final: 0.5469 (mt-10) REVERT: I 4 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8356 (mmm) REVERT: I 105 GLU cc_start: 0.5559 (tm-30) cc_final: 0.5155 (mt-10) REVERT: G 38 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7838 (ptt180) REVERT: K 105 GLU cc_start: 0.5587 (tm-30) cc_final: 0.5206 (mt-10) outliers start: 54 outliers final: 30 residues processed: 245 average time/residue: 0.5217 time to fit residues: 144.7287 Evaluate side-chains 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 195 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120251 restraints weight = 19052.478| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.90 r_work: 0.2900 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 18247 Z= 0.352 Angle : 0.873 33.110 24847 Z= 0.415 Chirality : 0.055 0.581 2786 Planarity : 0.005 0.055 3114 Dihedral : 8.136 80.807 3225 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.99 % Allowed : 25.30 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.48 (0.17), residues: 2142 helix: 1.83 (0.27), residues: 357 sheet: -0.11 (0.22), residues: 519 loop : -1.07 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 429 TYR 0.036 0.003 TYR K 27D PHE 0.015 0.003 PHE B 357 TRP 0.024 0.002 TRP C 375 HIS 0.007 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.35 (18185) covalent geometry : angle 0.83165 / 0.41 (24688) SS BOND : bond 0.00555 / 0.33 ( 21) SS BOND : angle 2.06286 / 1.26 ( 42) hydrogen bonds : bond 0.04755 / 3.12 ( 627) hydrogen bonds : angle 5.35469 / 3.74 ( 1770) Misc. bond : bond 0.00679 / 0.34 ( 2) link_ALPHA1-3 : bond 0.00845 / 0.43 ( 3) link_ALPHA1-3 : angle 1.24175 / 0.62 ( 9) link_ALPHA1-6 : bond 0.00640 / 0.32 ( 3) link_ALPHA1-6 : angle 1.45083 / 0.89 ( 9) link_BETA1-2 : bond 0.00281 / 0.14 ( 3) link_BETA1-2 : angle 1.45674 / 0.73 ( 9) link_BETA1-4 : bond 0.00685 / 0.38 ( 15) link_BETA1-4 : angle 3.46682 / 2.18 ( 45) link_BETA2-3 : bond 0.00781 / 0.39 ( 3) link_BETA2-3 : angle 6.89390 / 3.88 ( 9) link_NAG-ASN : bond 0.00756 / 0.46 ( 12) link_NAG-ASN : angle 4.24787 / 2.82 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6923.21 seconds wall clock time: 118 minutes 55.88 seconds (7135.88 seconds total)