Starting phenix.real_space_refine on Thu Jul 2 23:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty0_26163/07_2026/7ty0_26163.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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 66 5.16 5 C 6844 2.51 5 N 1854 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10640 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 458 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 69} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 414 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 704 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain breaks: 4 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "K" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 657 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 98} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Chain: "N" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 688 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 97} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "O" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 621 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 90} Chain breaks: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3380 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 453} Chain breaks: 4 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 17, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 7, 'ARG:plan': 3, 'ASN:plan1': 10, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 228 Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3389 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 16, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 14, 'GLN:plan1': 9, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 236 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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 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 chiralities: 3 Time building chain proxies: 2.19, per 1000 atoms: 0.21 Number of scatterers: 10640 At special positions: 0 Unit cell: (77.7, 144.9, 118.65, 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 66 16.00 O 1876 8.00 N 1854 7.00 C 6844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 92 " distance=2.08 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 601 " distance=2.03 Simple disulfide: pdb=" SG CYS D 216 " - pdb=" SG CYS D 240 " distance=2.04 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 395 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 499 " distance=2.02 Simple disulfide: pdb=" SG CYS D 493 " - pdb=" SG CYS D 503 " distance=2.03 Simple disulfide: pdb=" SG CYS D 565 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 240 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 395 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 499 " distance=2.04 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 503 " distance=2.05 Simple disulfide: pdb=" SG CYS C 565 " - pdb=" SG CYS C 574 " 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 701 " - " ASN C 378 " " NAG C 702 " - " ASN C 481 " " NAG C 703 " - " ASN C 529 " " NAG D 701 " - " ASN D 378 " " NAG D 702 " - " ASN D 159 " " NAG D 703 " - " ASN D 417 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN B 159 " " NAG G 1 " - " ASN D 306 " " NAG H 1 " - " ASN D 481 " " NAG I 1 " - " ASN D 529 " " NAG L 1 " - " ASN C 306 " " NAG M 1 " - " ASN C 417 " " NAG P 1 " - " ASN C 159 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 272.0 milliseconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 28 sheets defined 19.4% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 105 through 118 removed outlier: 4.098A pdb=" N LEU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 146 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 118 through 146 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.773A pdb=" N ILE O 87 " --> pdb=" O GLU O 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 146 Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 327 through 330 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'C' and resid 98 through 104 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 118 through 146 Processing helix chain 'C' and resid 204 through 207 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 393 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'J' and resid 60 through 61 removed outlier: 6.591A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS J 98 " --> pdb=" O TRP J 109 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP J 109 " --> pdb=" O CYS J 98 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG J 100 " --> pdb=" O ALA J 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 60 through 61 removed outlier: 6.591A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.936A pdb=" N TRP K 33 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET K 34 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.854A pdb=" N CYS K 98 " --> pdb=" O TRP K 109 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP K 109 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG K 100 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.004A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'O' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'O' and resid 49 through 52 removed outlier: 5.532A pdb=" N LEU O 50 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN O 41 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 49 through 52 removed outlier: 5.532A pdb=" N LEU O 50 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN O 41 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 178 through 180 removed outlier: 5.040A pdb=" N LYS D 560 " --> pdb=" O GLU D 579 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 225 removed outlier: 6.404A pdb=" N SER D 232 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 222 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA D 230 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET D 224 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR D 228 " --> pdb=" O MET D 224 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE D 229 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 252 " --> pdb=" O PHE D 229 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR D 231 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE D 250 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS D 233 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG D 248 " --> pdb=" O HIS D 233 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU D 235 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 244 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU D 254 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET D 267 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 256 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU D 265 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 287 removed outlier: 5.618A pdb=" N HIS D 281 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA D 296 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 340 through 341 removed outlier: 3.577A pdb=" N LYS D 347 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 341 Processing sheet with id=AC2, first strand: chain 'D' and resid 442 through 447 removed outlier: 4.124A pdb=" N LYS D 465 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 468 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 476 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 512 through 515 removed outlier: 6.820A pdb=" N ILE D 520 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 547 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS D 541 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 178 through 179 removed outlier: 6.652A pdb=" N ALA C 558 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR C 581 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS C 560 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 215 through 225 removed outlier: 6.485A pdb=" N SER C 232 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 222 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 230 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET C 224 " --> pdb=" O TYR C 228 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 228 " --> pdb=" O MET C 224 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 229 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 252 " --> pdb=" O PHE C 229 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 231 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 250 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS C 233 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG C 248 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU C 235 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 244 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU C 254 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N MET C 267 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 256 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU C 265 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 279 through 287 removed outlier: 5.608A pdb=" N HIS C 281 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA C 296 " --> pdb=" O HIS C 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AC9, first strand: chain 'C' and resid 442 through 447 removed outlier: 4.354A pdb=" N LYS C 465 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 468 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 476 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 512 through 515 removed outlier: 6.740A pdb=" N ILE C 520 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 547 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 541 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2705 1.33 - 1.46: 3326 1.46 - 1.60: 4758 1.60 - 1.73: 2 1.73 - 1.87: 84 Bond restraints: 10875 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" NE ARG D 548 " pdb=" CZ ARG D 548 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" C1 NAG C 703 " pdb=" C2 NAG C 703 " ideal model delta sigma weight residual 1.532 1.608 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" NE ARG D 487 " pdb=" CZ ARG D 487 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.38e+01 bond pdb=" NE ARG J 69 " pdb=" CZ ARG J 69 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.19e+01 ... (remaining 10870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 14519 4.03 - 8.06: 358 8.06 - 12.09: 5 12.09 - 16.11: 0 16.11 - 20.14: 1 Bond angle restraints: 14883 Sorted by residual: angle pdb=" CG1 VAL C 209 " pdb=" CB VAL C 209 " pdb=" CG2 VAL C 209 " ideal model delta sigma weight residual 110.80 130.94 -20.14 2.20e+00 2.07e-01 8.38e+01 angle pdb=" C CYS C 493 " pdb=" N PRO C 494 " pdb=" CA PRO C 494 " ideal model delta sigma weight residual 120.03 128.47 -8.44 9.90e-01 1.02e+00 7.27e+01 angle pdb=" C ASN C 275 " pdb=" N PRO C 276 " pdb=" CA PRO C 276 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.02e+00 9.61e-01 5.73e+01 angle pdb=" C GLY A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta sigma weight residual 119.56 127.03 -7.47 1.02e+00 9.61e-01 5.36e+01 angle pdb=" C LYS D 322 " pdb=" N PRO D 323 " pdb=" CA PRO D 323 " ideal model delta sigma weight residual 120.03 127.21 -7.18 9.90e-01 1.02e+00 5.25e+01 ... (remaining 14878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6042 17.95 - 35.89: 125 35.89 - 53.84: 42 53.84 - 71.78: 5 71.78 - 89.73: 5 Dihedral angle restraints: 6219 sinusoidal: 1838 harmonic: 4381 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 166.68 -73.68 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS B 146 " pdb=" SG CYS B 146 " pdb=" SG CYS D 146 " pdb=" CB CYS D 146 " ideal model delta sinusoidal sigma weight residual 93.00 142.53 -49.53 1 1.00e+01 1.00e-02 3.37e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.46 44.54 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 6216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 1746 0.293 - 0.586: 27 0.586 - 0.879: 1 0.879 - 1.173: 1 1.173 - 1.466: 1 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.33e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.07e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.17e+01 ... (remaining 1773 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 529 " 0.124 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" CG ASN C 529 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 529 " 0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN C 529 " -0.427 2.00e-02 2.50e+03 pdb=" C1 NAG C 703 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 159 " -0.112 2.00e-02 2.50e+03 1.83e-01 4.19e+02 pdb=" CG ASN C 159 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN C 159 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN C 159 " 0.324 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 481 " -0.039 2.00e-02 2.50e+03 4.67e-02 2.72e+01 pdb=" CG ASN D 481 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN D 481 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 481 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.058 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4224 2.91 - 3.41: 9120 3.41 - 3.91: 17275 3.91 - 4.40: 19318 4.40 - 4.90: 32191 Nonbonded interactions: 82128 Sorted by model distance: nonbonded pdb=" O ARG D 435 " pdb=" NZ LYS D 465 " model vdw 2.417 3.120 nonbonded pdb=" N SER C 440 " pdb=" O SER C 440 " model vdw 2.447 2.496 nonbonded pdb=" OE1 GLN C 455 " pdb=" NZ LYS C 465 " model vdw 2.467 3.120 nonbonded pdb=" N PHE D 458 " pdb=" N SER D 459 " model vdw 2.525 2.560 nonbonded pdb=" O VAL C 182 " pdb=" N LEU C 184 " model vdw 2.533 3.120 ... (remaining 82123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 96 through 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 131 or (resid 132 and (name N or name CA or \ name C or name O or name CB )) or resid 133 through 141 or (resid 142 through 14 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 145 through \ 163)) selection = (chain 'B' and (resid 96 through 112 or (resid 113 through 119 and (name N or na \ me CA or name C or name O or name CB )) or resid 120 through 152 or (resid 153 t \ hrough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163)) } ncs_group { reference = (chain 'C' and (resid 97 through 113 or (resid 114 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 or (resid 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 131 or (resid 1 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 133 through \ 153 or (resid 154 through 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 208 or (resid 209 through 210 and ( \ name N or name CA or name C or name O or name CB )) or resid 211 or (resid 212 t \ hrough 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 237 or resid 240 through 253 or (resid 254 and (name N or name CA or na \ me C or name O or name CB )) or resid 255 through 278 or (resid 279 and (name N \ or name CA or name C or name O or name CB )) or resid 280 through 284 or (resid \ 285 and (name N or name CA or name C or name O or name CB )) or resid 286 throug \ h 339 or (resid 340 through 342 and (name N or name CA or name C or name O or na \ me CB )) or resid 343 or (resid 344 and (name N or name CA or name C or name O o \ r name CB )) or resid 345 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 378 or (resid 379 through 381 \ and (name N or name CA or name C or name O or name CB )) or resid 382 through 42 \ 4 or (resid 425 and (name N or name CA or name C or name O or name CB )) or resi \ d 426 through 467 or (resid 468 and (name N or name CA or name C or name O or na \ me CB )) or resid 469 through 477 or (resid 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 through 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 520 or (resid 521 \ through 522 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 3 through 526 or (resid 527 through 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 532 or (resid 533 and (name N or name CA o \ r name C or name O or name CB )) or resid 534 through 569 or (resid 570 and (nam \ e N or name CA or name C or name O or name CB )) or resid 571 through 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 or \ (resid 580 through 582 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 703)) selection = (chain 'D' and (resid 97 through 133 or (resid 134 through 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 179 or (resid 180 a \ nd (name N or name CA or name C or name O or name CB )) or resid 181 through 186 \ or (resid 187 through 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 or (resid 190 through 191 and (name N or name CA or name C or n \ ame O or name CB )) or resid 192 through 194 or (resid 195 through 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 202 or (res \ id 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thr \ ough 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) \ or resid 265 through 286 or (resid 287 through 289 and (name N or name CA or nam \ e C or name O or name CB )) or resid 290 through 312 or (resid 313 and (name N o \ r name CA or name C or name O or name CB )) or resid 314 through 371 or (resid 3 \ 72 through 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 or (resid 376 and (name N or name CA or name C or name O or name CB )) or r \ esid 377 through 383 or (resid 384 through 386 and (name N or name CA or name C \ or name O or name CB )) or resid 387 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 401 or (resid 402 a \ nd (name N or name CA or name C or name O or name CB )) or resid 403 through 410 \ or (resid 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 419 or resid 424 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB )) or resid 435 through 446 or (resid 447 and (nam \ e N or name CA or name C or name O or name CB )) or resid 448 through 456 or (re \ sid 457 and (name N or name CA or name C or name O or name CB )) or resid 458 th \ rough 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) \ or resid 463 through 490 or resid 492 through 496 or (resid 497 through 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 504 o \ r (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 06 through 519 or (resid 520 through 522 and (name N or name CA or name C or nam \ e O or name CB )) or resid 523 through 529 or (resid 530 through 533 and (name N \ or name CA or name C or name O or name CB )) or resid 534 through 541 or (resid \ 542 through 544 and (name N or name CA or name C or name O or name CB )) or res \ id 545 through 560 or (resid 561 and (name N or name CA or name C or name O or n \ ame CB )) or resid 562 through 568 or (resid 569 through 570 and (name N or name \ CA or name C or name O or name CB )) or resid 571 through 703)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } ncs_group { reference = (chain 'J' and (resid 2 through 9 or resid 15 or (resid 18 through 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 29 or (resid \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 through 37 or (resid 38 and (name N or name CA or name C or name O or name \ CB )) or resid 39 through 62 or (resid 69 through 73 and (name N or name CA or n \ ame C or name O or name CB )) or resid 74 through 84 or (resid 85 through 86 and \ (name N or name CA or name C or name O or name CB )) or (resid 92 through 95 an \ d (name N or name CA or name C or name O or name CB )) or resid 96 through 100 o \ r (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 02 or (resid 103 through 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 116)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or resid 18 through 39 or (resid 45 through 46 \ and (name N or name CA or name C or name O or name CB )) or resid 47 through 62 \ or resid 69 through 75 or resid 78 through 82 or (resid 83 through 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 116)) } ncs_group { reference = (chain 'N' and (resid 2 through 6 or resid 17 through 23 or (resid 24 through 31 \ and (name N or name CA or name C or name O or name CB )) or resid 32 through 44 \ or (resid 46 and (name N or name CA or name C or name O or name CB )) or resid \ 47 through 51 or (resid 52 and (name N or name CA or name C or name O or name CB \ )) or resid 53 through 60 or resid 62 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 77 or (resid 78 thro \ ugh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 85 or (resid 86 through 89 and (name N or name CA or name C or name O or nam \ e CB )) or resid 90 through 110)) selection = (chain 'O' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 29 or (resid 30 through 31 and (name N or name CA \ or name C or name O or name CB )) or resid 32 through 42 or (resid 43 and (name \ N or name CA or name C or name O or name CB )) or resid 44 through 103 or resid \ 106 through 110)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.013 0.153 10923 Z= 0.732 Angle : 1.568 25.952 15003 Z= 1.000 Chirality : 0.105 1.466 1776 Planarity : 0.006 0.026 1908 Dihedral : 8.961 89.727 3323 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Rotamer: Outliers : 0.39 % Allowed : 1.94 % Favored : 97.67 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.05 % 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: 0.78 (0.21), residues: 1462 helix: 1.59 (0.37), residues: 194 sheet: 0.93 (0.23), residues: 475 loop : 0.06 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 487 TYR 0.049 0.006 TYR D 454 PHE 0.025 0.004 PHE C 525 TRP 0.023 0.005 TRP D 573 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01304 / 0.71 (10875) covalent geometry : angle 1.50285 / 0.99 (14883) SS BOND : bond 0.01189 / 0.91 ( 24) SS BOND : angle 3.16207 / 2.38 ( 48) hydrogen bonds : bond 0.15800 / 11.11 ( 524) hydrogen bonds : angle 8.12646 / 5.96 ( 1518) link_BETA1-4 : bond 0.06911 / 4.82 ( 9) link_BETA1-4 : angle 3.80492 / 2.63 ( 27) link_BETA1-6 : bond 0.06569 / 4.11 ( 1) link_BETA1-6 : angle 2.68352 / 0.98 ( 3) link_NAG-ASN : bond 0.07103 / 5.06 ( 14) link_NAG-ASN : angle 7.52315 / 5.17 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.394 Fit side-chains REVERT: J 108 TYR cc_start: 0.8012 (m-80) cc_final: 0.7776 (m-80) REVERT: N 75 PHE cc_start: 0.7235 (m-80) cc_final: 0.6934 (m-80) REVERT: D 399 MET cc_start: 0.8217 (mmm) cc_final: 0.7942 (mmm) REVERT: C 533 GLU cc_start: 0.7996 (pt0) cc_final: 0.7795 (pt0) outliers start: 3 outliers final: 1 residues processed: 222 average time/residue: 0.0838 time to fit residues: 26.6672 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 306 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 57 ASN D 187 ASN D 406 HIS D 518 ASN D 564 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124552 restraints weight = 15142.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126389 restraints weight = 12161.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126830 restraints weight = 9681.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127072 restraints weight = 9348.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127364 restraints weight = 9329.753| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10923 Z= 0.166 Angle : 0.739 16.235 15003 Z= 0.367 Chirality : 0.052 0.567 1776 Planarity : 0.005 0.047 1908 Dihedral : 4.929 42.402 1598 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.85 % Allowed : 8.41 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.91 (0.21), residues: 1462 helix: 3.20 (0.38), residues: 193 sheet: 0.66 (0.22), residues: 484 loop : -0.04 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 402 TYR 0.025 0.002 TYR D 351 PHE 0.019 0.002 PHE C 369 TRP 0.016 0.001 TRP C 271 HIS 0.003 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10875) covalent geometry : angle 0.67414 / 0.35 (14883) SS BOND : bond 0.00409 / 0.33 ( 24) SS BOND : angle 2.00994 / 1.50 ( 48) hydrogen bonds : bond 0.04284 / 3.08 ( 524) hydrogen bonds : angle 5.69768 / 4.19 ( 1518) link_BETA1-4 : bond 0.00683 / 0.46 ( 9) link_BETA1-4 : angle 1.92231 / 1.40 ( 27) link_BETA1-6 : bond 0.01018 / 0.64 ( 1) link_BETA1-6 : angle 1.28656 / 0.65 ( 3) link_NAG-ASN : bond 0.01031 / 0.79 ( 14) link_NAG-ASN : angle 5.17760 / 3.76 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 89 MET cc_start: 0.7649 (mmm) cc_final: 0.7436 (mmm) REVERT: N 93 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 190 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7280 (pp) REVERT: C 533 GLU cc_start: 0.8284 (pt0) cc_final: 0.8012 (pt0) REVERT: C 550 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7432 (mm-40) outliers start: 22 outliers final: 10 residues processed: 150 average time/residue: 0.0744 time to fit residues: 16.6879 Evaluate side-chains 121 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 142 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123146 restraints weight = 15234.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124536 restraints weight = 12076.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124745 restraints weight = 9589.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125102 restraints weight = 9715.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125229 restraints weight = 9216.301| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10923 Z= 0.143 Angle : 0.624 14.017 15003 Z= 0.313 Chirality : 0.048 0.393 1776 Planarity : 0.004 0.058 1908 Dihedral : 4.596 43.688 1598 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.23 % Allowed : 9.70 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.81 (0.22), residues: 1462 helix: 3.48 (0.39), residues: 194 sheet: 0.48 (0.22), residues: 474 loop : -0.13 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 487 TYR 0.016 0.001 TYR D 351 PHE 0.017 0.002 PHE O 91 TRP 0.014 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10875) covalent geometry : angle 0.58333 / 0.30 (14883) SS BOND : bond 0.00325 / 0.24 ( 24) SS BOND : angle 1.58426 / 1.22 ( 48) hydrogen bonds : bond 0.03538 / 2.55 ( 524) hydrogen bonds : angle 5.15730 / 3.79 ( 1518) link_BETA1-4 : bond 0.00577 / 0.39 ( 9) link_BETA1-4 : angle 1.55376 / 1.10 ( 27) link_BETA1-6 : bond 0.01171 / 0.73 ( 1) link_BETA1-6 : angle 1.28686 / 0.72 ( 3) link_NAG-ASN : bond 0.00788 / 0.63 ( 14) link_NAG-ASN : angle 3.73268 / 3.02 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7747 (tm-30) REVERT: D 291 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7585 (t80) REVERT: D 505 GLU cc_start: 0.7800 (pm20) cc_final: 0.7407 (pm20) REVERT: C 550 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7416 (mm-40) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 0.0733 time to fit residues: 16.2460 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 564 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 518 ASN C 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121800 restraints weight = 15449.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123185 restraints weight = 12196.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123345 restraints weight = 9888.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123509 restraints weight = 9981.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123585 restraints weight = 9603.106| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10923 Z= 0.147 Angle : 0.630 17.228 15003 Z= 0.305 Chirality : 0.048 0.350 1776 Planarity : 0.004 0.058 1908 Dihedral : 4.451 45.159 1598 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.88 % Allowed : 10.09 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.64 (0.22), residues: 1462 helix: 3.57 (0.38), residues: 192 sheet: 0.28 (0.22), residues: 493 loop : -0.24 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 396 TYR 0.022 0.001 TYR C 602 PHE 0.018 0.002 PHE J 70 TRP 0.016 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10875) covalent geometry : angle 0.57794 / 0.29 (14883) SS BOND : bond 0.00346 / 0.28 ( 24) SS BOND : angle 1.02977 / 0.85 ( 48) hydrogen bonds : bond 0.03150 / 2.27 ( 524) hydrogen bonds : angle 4.86559 / 3.58 ( 1518) link_BETA1-4 : bond 0.00492 / 0.34 ( 9) link_BETA1-4 : angle 1.38309 / 1.01 ( 27) link_BETA1-6 : bond 0.01152 / 0.72 ( 1) link_BETA1-6 : angle 1.34493 / 0.76 ( 3) link_NAG-ASN : bond 0.00521 / 0.39 ( 14) link_NAG-ASN : angle 4.54362 / 3.89 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7824 (tm-30) REVERT: N 94 GLN cc_start: 0.8364 (tp40) cc_final: 0.7615 (tm-30) REVERT: D 291 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7771 (t80) REVERT: D 505 GLU cc_start: 0.7661 (pm20) cc_final: 0.7364 (pm20) REVERT: C 455 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: C 550 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7640 (mm-40) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 0.0706 time to fit residues: 16.2087 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 61 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 ASN C 564 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130478 restraints weight = 15267.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130185 restraints weight = 18628.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131358 restraints weight = 18680.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132030 restraints weight = 11425.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133244 restraints weight = 10105.507| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10923 Z= 0.134 Angle : 0.601 16.463 15003 Z= 0.293 Chirality : 0.047 0.327 1776 Planarity : 0.004 0.058 1908 Dihedral : 4.378 46.054 1598 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.23 % Allowed : 11.64 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.60 (0.22), residues: 1462 helix: 3.55 (0.38), residues: 193 sheet: 0.28 (0.22), residues: 488 loop : -0.29 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 487 TYR 0.034 0.001 TYR D 377 PHE 0.014 0.001 PHE C 369 TRP 0.015 0.001 TRP C 519 HIS 0.002 0.000 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10875) covalent geometry : angle 0.55623 / 0.28 (14883) SS BOND : bond 0.00212 / 0.16 ( 24) SS BOND : angle 0.86900 / 0.70 ( 48) hydrogen bonds : bond 0.02996 / 2.16 ( 524) hydrogen bonds : angle 4.74619 / 3.48 ( 1518) link_BETA1-4 : bond 0.00516 / 0.35 ( 9) link_BETA1-4 : angle 1.30680 / 0.96 ( 27) link_BETA1-6 : bond 0.01192 / 0.75 ( 1) link_BETA1-6 : angle 1.30349 / 0.73 ( 3) link_NAG-ASN : bond 0.00609 / 0.48 ( 14) link_NAG-ASN : angle 4.17037 / 3.56 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 94 GLN cc_start: 0.8275 (tp40) cc_final: 0.7657 (tm-30) REVERT: D 291 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7679 (t80) REVERT: D 399 MET cc_start: 0.7871 (tpp) cc_final: 0.7636 (tpp) REVERT: D 505 GLU cc_start: 0.7669 (pm20) cc_final: 0.7249 (pm20) REVERT: C 455 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: C 550 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7662 (mm-40) outliers start: 25 outliers final: 17 residues processed: 135 average time/residue: 0.0751 time to fit residues: 15.5133 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 564 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 62 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130115 restraints weight = 15448.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129879 restraints weight = 17588.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131086 restraints weight = 14301.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131565 restraints weight = 10602.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132165 restraints weight = 10318.518| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10923 Z= 0.128 Angle : 0.572 12.778 15003 Z= 0.283 Chirality : 0.048 0.555 1776 Planarity : 0.004 0.059 1908 Dihedral : 4.282 46.208 1598 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.98 % Allowed : 12.81 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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 (0.22), residues: 1462 helix: 3.58 (0.39), residues: 193 sheet: 0.23 (0.22), residues: 499 loop : -0.30 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.015 0.001 TYR N 32 PHE 0.014 0.001 PHE C 369 TRP 0.015 0.001 TRP C 271 HIS 0.002 0.000 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10875) covalent geometry : angle 0.54336 / 0.28 (14883) SS BOND : bond 0.00209 / 0.16 ( 24) SS BOND : angle 0.79807 / 0.60 ( 48) hydrogen bonds : bond 0.02946 / 2.14 ( 524) hydrogen bonds : angle 4.69493 / 3.45 ( 1518) link_BETA1-4 : bond 0.00457 / 0.31 ( 9) link_BETA1-4 : angle 1.27975 / 0.94 ( 27) link_BETA1-6 : bond 0.01154 / 0.72 ( 1) link_BETA1-6 : angle 1.33358 / 0.75 ( 3) link_NAG-ASN : bond 0.00630 / 0.49 ( 14) link_NAG-ASN : angle 3.23577 / 2.66 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7694 (tm-30) REVERT: N 94 GLN cc_start: 0.8295 (tp40) cc_final: 0.7723 (tm-30) REVERT: D 291 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7673 (t80) REVERT: D 399 MET cc_start: 0.7922 (tpp) cc_final: 0.7632 (tpp) REVERT: D 463 MET cc_start: 0.7001 (mmm) cc_final: 0.6663 (mmp) REVERT: D 505 GLU cc_start: 0.7507 (pm20) cc_final: 0.6946 (pm20) REVERT: C 455 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: C 550 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7712 (mm-40) outliers start: 23 outliers final: 19 residues processed: 133 average time/residue: 0.0699 time to fit residues: 14.1170 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 0.0470 chunk 47 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130016 restraints weight = 15299.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129389 restraints weight = 17659.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130657 restraints weight = 17719.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131072 restraints weight = 11199.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131890 restraints weight = 10121.420| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10923 Z= 0.116 Angle : 0.546 12.597 15003 Z= 0.273 Chirality : 0.046 0.324 1776 Planarity : 0.004 0.059 1908 Dihedral : 4.209 46.506 1598 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.23 % Allowed : 12.94 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.60 (0.22), residues: 1462 helix: 3.63 (0.39), residues: 193 sheet: 0.31 (0.22), residues: 506 loop : -0.35 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.016 0.001 TYR N 32 PHE 0.013 0.001 PHE C 369 TRP 0.014 0.001 TRP C 271 HIS 0.002 0.000 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10875) covalent geometry : angle 0.52156 / 0.27 (14883) SS BOND : bond 0.00195 / 0.14 ( 24) SS BOND : angle 0.65156 / 0.47 ( 48) hydrogen bonds : bond 0.02793 / 2.02 ( 524) hydrogen bonds : angle 4.57552 / 3.35 ( 1518) link_BETA1-4 : bond 0.00447 / 0.31 ( 9) link_BETA1-4 : angle 1.24347 / 0.92 ( 27) link_BETA1-6 : bond 0.01174 / 0.73 ( 1) link_BETA1-6 : angle 1.31857 / 0.75 ( 3) link_NAG-ASN : bond 0.00444 / 0.33 ( 14) link_NAG-ASN : angle 2.92808 / 2.36 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 ASN cc_start: 0.8825 (m-40) cc_final: 0.8587 (m-40) REVERT: N 94 GLN cc_start: 0.8347 (tp40) cc_final: 0.7773 (tm-30) REVERT: O 93 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 234 LEU cc_start: 0.7911 (tt) cc_final: 0.7699 (tp) REVERT: D 291 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7706 (t80) REVERT: D 399 MET cc_start: 0.7923 (tpp) cc_final: 0.7570 (tpp) REVERT: D 463 MET cc_start: 0.7023 (mmm) cc_final: 0.6725 (mmp) REVERT: D 505 GLU cc_start: 0.7410 (pm20) cc_final: 0.6889 (pm20) REVERT: C 455 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: C 550 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7702 (mm-40) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.0648 time to fit residues: 13.2011 Evaluate side-chains 124 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 146 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 187 ASN D 287 ASN C 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127452 restraints weight = 15457.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126907 restraints weight = 17952.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128191 restraints weight = 14380.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128653 restraints weight = 10918.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129266 restraints weight = 10485.067| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10923 Z= 0.169 Angle : 0.585 12.424 15003 Z= 0.295 Chirality : 0.047 0.335 1776 Planarity : 0.004 0.060 1908 Dihedral : 4.391 45.601 1598 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.98 % Allowed : 13.84 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.53 (0.22), residues: 1462 helix: 3.44 (0.38), residues: 193 sheet: 0.37 (0.23), residues: 493 loop : -0.44 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 487 TYR 0.014 0.001 TYR N 32 PHE 0.017 0.002 PHE C 369 TRP 0.017 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10875) covalent geometry : angle 0.56193 / 0.29 (14883) SS BOND : bond 0.00270 / 0.21 ( 24) SS BOND : angle 0.80703 / 0.60 ( 48) hydrogen bonds : bond 0.03090 / 2.22 ( 524) hydrogen bonds : angle 4.77679 / 3.49 ( 1518) link_BETA1-4 : bond 0.00417 / 0.28 ( 9) link_BETA1-4 : angle 1.32968 / 0.99 ( 27) link_BETA1-6 : bond 0.01151 / 0.72 ( 1) link_BETA1-6 : angle 1.43446 / 0.82 ( 3) link_NAG-ASN : bond 0.00388 / 0.28 ( 14) link_NAG-ASN : angle 2.86904 / 2.26 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 94 GLN cc_start: 0.8444 (tp40) cc_final: 0.7997 (tm-30) REVERT: O 93 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 234 LEU cc_start: 0.7923 (tt) cc_final: 0.7704 (tp) REVERT: D 291 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 463 MET cc_start: 0.7123 (mmm) cc_final: 0.6871 (mmp) REVERT: D 505 GLU cc_start: 0.7431 (pm20) cc_final: 0.6798 (pm20) REVERT: C 455 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 550 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7820 (mm-40) outliers start: 23 outliers final: 19 residues processed: 129 average time/residue: 0.0717 time to fit residues: 14.1375 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 478 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN C 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127782 restraints weight = 15494.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127554 restraints weight = 18928.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129306 restraints weight = 14259.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129556 restraints weight = 10373.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130205 restraints weight = 9934.892| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10923 Z= 0.161 Angle : 0.571 12.368 15003 Z= 0.288 Chirality : 0.047 0.332 1776 Planarity : 0.004 0.055 1908 Dihedral : 4.365 45.736 1598 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.98 % Allowed : 14.62 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.44 (0.22), residues: 1462 helix: 3.44 (0.38), residues: 193 sheet: 0.36 (0.23), residues: 486 loop : -0.54 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.018 0.002 TYR K 32 PHE 0.016 0.002 PHE C 369 TRP 0.015 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10875) covalent geometry : angle 0.54857 / 0.28 (14883) SS BOND : bond 0.00291 / 0.23 ( 24) SS BOND : angle 0.75344 / 0.57 ( 48) hydrogen bonds : bond 0.03046 / 2.20 ( 524) hydrogen bonds : angle 4.75733 / 3.48 ( 1518) link_BETA1-4 : bond 0.00459 / 0.32 ( 9) link_BETA1-4 : angle 1.28283 / 0.96 ( 27) link_BETA1-6 : bond 0.01221 / 0.76 ( 1) link_BETA1-6 : angle 1.37618 / 0.78 ( 3) link_NAG-ASN : bond 0.00431 / 0.32 ( 14) link_NAG-ASN : angle 2.85025 / 2.25 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7755 (tm-30) REVERT: N 94 GLN cc_start: 0.8470 (tp40) cc_final: 0.7952 (tm-30) REVERT: O 93 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 234 LEU cc_start: 0.7938 (tt) cc_final: 0.7715 (tp) REVERT: D 291 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7849 (t80) REVERT: D 463 MET cc_start: 0.7132 (mmm) cc_final: 0.6879 (mmt) REVERT: D 505 GLU cc_start: 0.7368 (pm20) cc_final: 0.6855 (pm20) REVERT: C 455 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: C 550 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7844 (mm-40) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.0680 time to fit residues: 12.9885 Evaluate side-chains 121 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127186 restraints weight = 15473.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125236 restraints weight = 17536.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126159 restraints weight = 17569.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127995 restraints weight = 11890.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128068 restraints weight = 10186.669| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10923 Z= 0.143 Angle : 0.563 12.212 15003 Z= 0.282 Chirality : 0.046 0.320 1776 Planarity : 0.004 0.056 1908 Dihedral : 4.304 45.606 1598 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.98 % Allowed : 14.75 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.45 (0.22), residues: 1462 helix: 3.47 (0.39), residues: 193 sheet: 0.40 (0.23), residues: 478 loop : -0.57 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.015 0.001 TYR N 32 PHE 0.016 0.002 PHE C 369 TRP 0.024 0.001 TRP C 519 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10875) covalent geometry : angle 0.54060 / 0.28 (14883) SS BOND : bond 0.00335 / 0.27 ( 24) SS BOND : angle 0.83785 / 0.68 ( 48) hydrogen bonds : bond 0.02905 / 2.09 ( 524) hydrogen bonds : angle 4.69274 / 3.43 ( 1518) link_BETA1-4 : bond 0.00434 / 0.30 ( 9) link_BETA1-4 : angle 1.24270 / 0.93 ( 27) link_BETA1-6 : bond 0.01195 / 0.75 ( 1) link_BETA1-6 : angle 1.35910 / 0.77 ( 3) link_NAG-ASN : bond 0.00422 / 0.31 ( 14) link_NAG-ASN : angle 2.79470 / 2.21 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 ASN cc_start: 0.8852 (m-40) cc_final: 0.8604 (m-40) REVERT: B 158 CYS cc_start: 0.2400 (m) cc_final: 0.2081 (m) REVERT: J 69 ARG cc_start: 0.3060 (ptt-90) cc_final: 0.2761 (ptt-90) REVERT: N 93 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7689 (tm-30) REVERT: N 94 GLN cc_start: 0.8475 (tp40) cc_final: 0.7987 (tm-30) REVERT: O 93 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 234 LEU cc_start: 0.7948 (tt) cc_final: 0.7719 (tp) REVERT: D 291 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7912 (t80) REVERT: D 505 GLU cc_start: 0.7383 (pm20) cc_final: 0.6847 (pm20) REVERT: C 455 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: C 533 GLU cc_start: 0.8131 (pt0) cc_final: 0.7837 (pt0) REVERT: C 550 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7886 (mm-40) outliers start: 23 outliers final: 18 residues processed: 127 average time/residue: 0.0912 time to fit residues: 17.6312 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 519 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 28 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 53 optimal weight: 0.0070 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129456 restraints weight = 15438.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128312 restraints weight = 16750.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130297 restraints weight = 13786.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130523 restraints weight = 10070.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131125 restraints weight = 9691.367| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10923 Z= 0.098 Angle : 0.535 12.247 15003 Z= 0.266 Chirality : 0.046 0.310 1776 Planarity : 0.004 0.056 1908 Dihedral : 4.116 46.066 1598 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.59 % Allowed : 14.75 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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 (0.22), residues: 1462 helix: 3.60 (0.39), residues: 193 sheet: 0.48 (0.23), residues: 480 loop : -0.49 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.015 0.001 TYR N 32 PHE 0.019 0.001 PHE J 70 TRP 0.018 0.001 TRP C 271 HIS 0.003 0.000 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10875) covalent geometry : angle 0.51364 / 0.26 (14883) SS BOND : bond 0.00275 / 0.21 ( 24) SS BOND : angle 0.69647 / 0.54 ( 48) hydrogen bonds : bond 0.02625 / 1.89 ( 524) hydrogen bonds : angle 4.46869 / 3.28 ( 1518) link_BETA1-4 : bond 0.00445 / 0.31 ( 9) link_BETA1-4 : angle 1.17956 / 0.89 ( 27) link_BETA1-6 : bond 0.01187 / 0.74 ( 1) link_BETA1-6 : angle 1.29187 / 0.72 ( 3) link_NAG-ASN : bond 0.00473 / 0.35 ( 14) link_NAG-ASN : angle 2.67470 / 2.13 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.66 seconds wall clock time: 27 minutes 1.94 seconds (1621.94 seconds total)