Starting phenix.real_space_refine on Tue May 13 18:29:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_26163.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_26163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_26163.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_26163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty0_26163/05_2025/7ty0_26163.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 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, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} 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, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 3} 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: {'GLN:plan1': 9, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 14, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 16, 'ASP:plan': 17} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.86, per 1000 atoms: 0.74 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: 2.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.79 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: 4.44 Time building geometry restraints manager: 3.26 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 - 21.19: 6529 21.19 - 42.37: 145 42.37 - 63.56: 28 63.56 - 84.74: 9 84.74 - 105.93: 6 Dihedral angle restraints: 6717 sinusoidal: 2336 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 6714 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 602 or resid 701 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 602 or resid 701 thro \ ugh 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: 8.420 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: 0.180 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 10.108 105.929 3821 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (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 TRP 0.023 0.005 TRP D 573 HIS 0.002 0.001 HIS C 233 PHE 0.025 0.004 PHE C 525 TYR 0.049 0.006 TYR D 454 ARG 0.006 0.001 ARG D 487 Details of bonding type rmsd link_NAG-ASN : bond 0.07103 ( 14) link_NAG-ASN : angle 7.52315 ( 42) link_BETA1-4 : bond 0.06911 ( 9) link_BETA1-4 : angle 3.80492 ( 27) hydrogen bonds : bond 0.15800 ( 524) hydrogen bonds : angle 8.12646 ( 1518) link_BETA1-6 : bond 0.06569 ( 1) link_BETA1-6 : angle 2.68352 ( 3) SS BOND : bond 0.01189 ( 24) SS BOND : angle 3.16207 ( 48) covalent geometry : bond 0.01304 (10875) covalent geometry : angle 1.50285 (14883) *********************** 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 : 1.095 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: 0.2285 time to fit residues: 71.6171 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 : 1.243 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 0.1980 chunk 59 optimal weight: 0.0970 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.162051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134667 restraints weight = 15044.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133491 restraints weight = 16334.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134303 restraints weight = 17614.036| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10923 Z= 0.159 Angle : 0.727 15.552 15003 Z= 0.362 Chirality : 0.052 0.595 1776 Planarity : 0.005 0.045 1908 Dihedral : 7.558 70.882 2096 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.72 % Allowed : 8.67 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1462 helix: 3.16 (0.37), residues: 193 sheet: 0.66 (0.22), residues: 484 loop : -0.05 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 271 HIS 0.003 0.001 HIS D 233 PHE 0.020 0.002 PHE C 369 TYR 0.025 0.002 TYR D 351 ARG 0.004 0.001 ARG D 402 Details of bonding type rmsd link_NAG-ASN : bond 0.01076 ( 14) link_NAG-ASN : angle 4.79478 ( 42) link_BETA1-4 : bond 0.00735 ( 9) link_BETA1-4 : angle 2.09904 ( 27) hydrogen bonds : bond 0.04176 ( 524) hydrogen bonds : angle 5.68354 ( 1518) link_BETA1-6 : bond 0.01005 ( 1) link_BETA1-6 : angle 1.00114 ( 3) SS BOND : bond 0.00517 ( 24) SS BOND : angle 1.95948 ( 48) covalent geometry : bond 0.00343 (10875) covalent geometry : angle 0.66897 (14883) *********************** 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 161 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 190 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7315 (pp) REVERT: D 291 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7403 (t80) REVERT: C 533 GLU cc_start: 0.8292 (pt0) cc_final: 0.8031 (pt0) REVERT: C 550 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7382 (mm-40) outliers start: 21 outliers final: 11 residues processed: 154 average time/residue: 0.2131 time to fit residues: 50.2749 Evaluate side-chains 124 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS 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 291 TYR 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 81 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 76 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 136 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN D 518 ASN C 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124935 restraints weight = 15275.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124871 restraints weight = 12265.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124800 restraints weight = 10259.066| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10923 Z= 0.156 Angle : 0.639 14.155 15003 Z= 0.321 Chirality : 0.049 0.432 1776 Planarity : 0.004 0.057 1908 Dihedral : 6.402 48.845 2096 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.49 % Allowed : 10.35 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1462 helix: 3.37 (0.38), residues: 193 sheet: 0.44 (0.22), residues: 478 loop : -0.15 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 PHE 0.018 0.002 PHE C 369 TYR 0.016 0.002 TYR D 351 ARG 0.005 0.000 ARG C 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 14) link_NAG-ASN : angle 3.70911 ( 42) link_BETA1-4 : bond 0.00619 ( 9) link_BETA1-4 : angle 1.88521 ( 27) hydrogen bonds : bond 0.03562 ( 524) hydrogen bonds : angle 5.20532 ( 1518) link_BETA1-6 : bond 0.01203 ( 1) link_BETA1-6 : angle 0.97000 ( 3) SS BOND : bond 0.00293 ( 24) SS BOND : angle 1.75112 ( 48) covalent geometry : bond 0.00358 (10875) covalent geometry : angle 0.59697 (14883) *********************** 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 153 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7788 (tm-30) REVERT: D 291 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7841 (t80) REVERT: D 505 GLU cc_start: 0.7818 (pm20) cc_final: 0.7427 (pm20) REVERT: C 550 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7494 (mm-40) outliers start: 27 outliers final: 14 residues processed: 148 average time/residue: 0.1891 time to fit residues: 42.6577 Evaluate side-chains 128 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 CYS 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 470 LEU 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 210 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 472 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 ASN ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129643 restraints weight = 15269.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128086 restraints weight = 17185.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128882 restraints weight = 18445.964| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10923 Z= 0.186 Angle : 0.663 14.025 15003 Z= 0.324 Chirality : 0.050 0.456 1776 Planarity : 0.004 0.057 1908 Dihedral : 7.495 125.408 2096 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.27 % Allowed : 10.87 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1462 helix: 3.49 (0.38), residues: 192 sheet: 0.20 (0.22), residues: 493 loop : -0.27 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 271 HIS 0.002 0.001 HIS D 233 PHE 0.020 0.002 PHE J 70 TYR 0.026 0.002 TYR D 377 ARG 0.004 0.000 ARG C 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 14) link_NAG-ASN : angle 4.28590 ( 42) link_BETA1-4 : bond 0.00422 ( 9) link_BETA1-4 : angle 1.84519 ( 27) hydrogen bonds : bond 0.03417 ( 524) hydrogen bonds : angle 5.04503 ( 1518) link_BETA1-6 : bond 0.01155 ( 1) link_BETA1-6 : angle 1.05179 ( 3) SS BOND : bond 0.00336 ( 24) SS BOND : angle 1.49874 ( 48) covalent geometry : bond 0.00425 (10875) covalent geometry : angle 0.61452 (14883) *********************** 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 150 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 89 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6531 (tmm) REVERT: N 93 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7975 (tm-30) REVERT: N 94 GLN cc_start: 0.8327 (tp40) cc_final: 0.7659 (tm-30) REVERT: D 291 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7987 (t80) REVERT: D 505 GLU cc_start: 0.7751 (pm20) cc_final: 0.7348 (pm20) REVERT: C 455 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: C 550 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7706 (mm-40) outliers start: 33 outliers final: 18 residues processed: 142 average time/residue: 0.2120 time to fit residues: 45.0261 Evaluate side-chains 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain N residue 89 MET 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 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 77 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128112 restraints weight = 15343.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127390 restraints weight = 18456.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128496 restraints weight = 19128.575| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10923 Z= 0.179 Angle : 0.640 13.957 15003 Z= 0.314 Chirality : 0.048 0.391 1776 Planarity : 0.004 0.057 1908 Dihedral : 6.691 91.939 2096 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.88 % Allowed : 11.64 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1462 helix: 3.50 (0.38), residues: 192 sheet: 0.13 (0.22), residues: 494 loop : -0.37 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 271 HIS 0.002 0.001 HIS C 233 PHE 0.018 0.002 PHE C 369 TYR 0.021 0.002 TYR N 53 ARG 0.004 0.001 ARG C 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 14) link_NAG-ASN : angle 3.85539 ( 42) link_BETA1-4 : bond 0.00512 ( 9) link_BETA1-4 : angle 1.73663 ( 27) hydrogen bonds : bond 0.03320 ( 524) hydrogen bonds : angle 4.98323 ( 1518) link_BETA1-6 : bond 0.01210 ( 1) link_BETA1-6 : angle 1.03916 ( 3) SS BOND : bond 0.00377 ( 24) SS BOND : angle 1.41706 ( 48) covalent geometry : bond 0.00419 (10875) covalent geometry : angle 0.59890 (14883) *********************** 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 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 53 TYR cc_start: 0.8418 (p90) cc_final: 0.8147 (p90) REVERT: N 89 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6538 (tmm) REVERT: N 94 GLN cc_start: 0.8324 (tp40) cc_final: 0.7684 (tm-30) REVERT: D 291 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.8075 (t80) REVERT: C 455 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: C 550 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7762 (mm-40) outliers start: 30 outliers final: 22 residues processed: 136 average time/residue: 0.1866 time to fit residues: 38.4545 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain N residue 89 MET 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 221 LEU Chi-restraints excluded: chain D residue 291 TYR Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 438 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 141 optimal weight: 0.6980 chunk 136 optimal weight: 0.0010 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128679 restraints weight = 15327.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128084 restraints weight = 17881.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129915 restraints weight = 14167.757| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10923 Z= 0.138 Angle : 0.616 15.864 15003 Z= 0.297 Chirality : 0.047 0.375 1776 Planarity : 0.004 0.058 1908 Dihedral : 5.660 55.206 2096 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.23 % Allowed : 12.68 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1462 helix: 3.50 (0.39), residues: 194 sheet: 0.34 (0.23), residues: 481 loop : -0.45 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 271 HIS 0.003 0.001 HIS C 233 PHE 0.015 0.002 PHE J 70 TYR 0.021 0.001 TYR N 53 ARG 0.003 0.000 ARG D 487 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 14) link_NAG-ASN : angle 4.46891 ( 42) link_BETA1-4 : bond 0.00493 ( 9) link_BETA1-4 : angle 1.52810 ( 27) hydrogen bonds : bond 0.02955 ( 524) hydrogen bonds : angle 4.75273 ( 1518) link_BETA1-6 : bond 0.01197 ( 1) link_BETA1-6 : angle 1.05749 ( 3) SS BOND : bond 0.00300 ( 24) SS BOND : angle 1.12246 ( 48) covalent geometry : bond 0.00316 (10875) covalent geometry : angle 0.56369 (14883) *********************** 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 141 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 93 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7761 (tm-30) REVERT: N 94 GLN cc_start: 0.8424 (tp40) cc_final: 0.8032 (tm-30) REVERT: D 291 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7930 (t80) REVERT: D 463 MET cc_start: 0.7038 (mmm) cc_final: 0.6742 (mmp) REVERT: C 455 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: C 519 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.6787 (t60) REVERT: C 550 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7779 (mm-40) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.1896 time to fit residues: 39.0515 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 133 optimal weight: 0.0470 chunk 108 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119626 restraints weight = 15534.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121869 restraints weight = 11852.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122301 restraints weight = 9588.005| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3616 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= 0.120 Angle : 0.581 13.832 15003 Z= 0.283 Chirality : 0.047 0.374 1776 Planarity : 0.004 0.056 1908 Dihedral : 5.383 56.439 2096 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.23 % Allowed : 13.71 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1462 helix: 3.60 (0.39), residues: 193 sheet: 0.47 (0.23), residues: 489 loop : -0.52 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 271 HIS 0.003 0.000 HIS C 233 PHE 0.017 0.001 PHE J 70 TYR 0.015 0.001 TYR N 32 ARG 0.003 0.000 ARG D 487 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 14) link_NAG-ASN : angle 3.88831 ( 42) link_BETA1-4 : bond 0.00479 ( 9) link_BETA1-4 : angle 1.46435 ( 27) hydrogen bonds : bond 0.02804 ( 524) hydrogen bonds : angle 4.61328 ( 1518) link_BETA1-6 : bond 0.01223 ( 1) link_BETA1-6 : angle 1.08465 ( 3) SS BOND : bond 0.00270 ( 24) SS BOND : angle 0.95359 ( 48) covalent geometry : bond 0.00270 (10875) covalent geometry : angle 0.53877 (14883) *********************** 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 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 ASN cc_start: 0.8975 (m-40) cc_final: 0.8735 (m-40) REVERT: J 38 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.7493 (ptt90) REVERT: N 94 GLN cc_start: 0.8497 (tp40) cc_final: 0.7883 (tm-30) REVERT: O 93 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 291 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 455 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: C 550 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7714 (mm-40) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.1997 time to fit residues: 39.8440 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 : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain N residue 89 MET 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 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 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 13 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 35 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 = 0.3986 r_free = 0.3986 target = 0.156088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128641 restraints weight = 15300.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128118 restraints weight = 18143.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129241 restraints weight = 17821.349| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10923 Z= 0.128 Angle : 0.579 13.691 15003 Z= 0.282 Chirality : 0.047 0.380 1776 Planarity : 0.004 0.058 1908 Dihedral : 5.305 58.379 2096 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.23 % Allowed : 13.97 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1462 helix: 3.59 (0.39), residues: 193 sheet: 0.49 (0.23), residues: 487 loop : -0.58 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 519 HIS 0.003 0.001 HIS C 233 PHE 0.013 0.001 PHE C 369 TYR 0.014 0.001 TYR N 32 ARG 0.005 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 14) link_NAG-ASN : angle 3.67477 ( 42) link_BETA1-4 : bond 0.00464 ( 9) link_BETA1-4 : angle 1.44688 ( 27) hydrogen bonds : bond 0.02814 ( 524) hydrogen bonds : angle 4.59930 ( 1518) link_BETA1-6 : bond 0.01231 ( 1) link_BETA1-6 : angle 1.01913 ( 3) SS BOND : bond 0.00306 ( 24) SS BOND : angle 0.96391 ( 48) covalent geometry : bond 0.00293 (10875) covalent geometry : angle 0.54062 (14883) *********************** 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 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 ASN cc_start: 0.8816 (m-40) cc_final: 0.8579 (m-40) REVERT: N 93 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7837 (tm-30) REVERT: N 94 GLN cc_start: 0.8431 (tp40) cc_final: 0.7993 (tm-30) REVERT: O 93 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7302 (tm-30) REVERT: D 291 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7913 (t80) REVERT: C 455 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: C 533 GLU cc_start: 0.8103 (pt0) cc_final: 0.7812 (pt0) REVERT: C 550 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7749 (mm-40) outliers start: 25 outliers final: 21 residues processed: 126 average time/residue: 0.1986 time to fit residues: 37.6899 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain N residue 89 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.5896 > 50: distance: 39 - 137: 30.564 distance: 42 - 134: 26.058 distance: 66 - 73: 34.571 distance: 78 - 79: 11.675 distance: 78 - 84: 40.519 distance: 79 - 80: 36.535 distance: 79 - 82: 10.553 distance: 80 - 81: 15.183 distance: 80 - 85: 42.535 distance: 83 - 84: 39.610 distance: 85 - 86: 24.837 distance: 86 - 87: 25.082 distance: 87 - 88: 14.871 distance: 87 - 89: 23.364 distance: 89 - 90: 14.580 distance: 90 - 91: 12.101 distance: 90 - 93: 13.653 distance: 91 - 92: 50.534 distance: 91 - 98: 36.237 distance: 93 - 94: 16.786 distance: 94 - 95: 27.769 distance: 98 - 99: 35.640 distance: 98 - 104: 37.452 distance: 99 - 100: 11.317 distance: 99 - 102: 20.490 distance: 100 - 101: 39.123 distance: 100 - 105: 53.808 distance: 102 - 103: 54.070 distance: 105 - 106: 37.568 distance: 105 - 111: 46.092 distance: 106 - 107: 14.917 distance: 106 - 109: 56.972 distance: 107 - 108: 31.167 distance: 109 - 110: 20.218 distance: 110 - 111: 39.420 distance: 114 - 115: 21.579 distance: 114 - 121: 5.501 distance: 116 - 117: 55.052 distance: 119 - 120: 36.812 distance: 121 - 122: 35.146 distance: 122 - 123: 50.188 distance: 122 - 125: 37.767 distance: 123 - 124: 51.488 distance: 123 - 129: 18.579 distance: 125 - 126: 11.013 distance: 126 - 127: 13.311 distance: 126 - 128: 38.224 distance: 129 - 130: 34.440 distance: 130 - 131: 6.210 distance: 130 - 133: 30.195 distance: 131 - 132: 13.625 distance: 131 - 134: 6.920 distance: 134 - 135: 34.663 distance: 135 - 136: 39.166 distance: 135 - 138: 13.674 distance: 136 - 137: 34.231 distance: 136 - 142: 31.897 distance: 138 - 139: 43.828 distance: 138 - 140: 25.194 distance: 139 - 141: 9.853