Starting phenix.real_space_refine on Fri Mar 6 09:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dim_27440/03_2026/8dim_27440.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15825 atoms to isotropic. 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 78 5.16 5 C 10549 2.51 5 N 2821 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16745 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3824 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 903 Chain: "G" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3824 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 903 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" 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: "K" 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "G" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.26 Number of scatterers: 16745 At special positions: 0 Unit cell: (132.3, 131.625, 142.425, 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 78 16.00 O 3297 8.00 N 2821 7.00 C 10549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 492 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 72 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 488 " - pdb=" SG CYS G 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 40 " " NAG A 603 " - " ASN A 498 " " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 40 " " NAG D 603 " - " ASN D 498 " " NAG G 601 " - " ASN G 28 " " NAG G 602 " - " ASN G 40 " " NAG G 603 " - " ASN G 498 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN D 104 " " NAG L 1 " - " ASN G 104 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 699.8 milliseconds 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3898 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 48 sheets defined 18.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 81 through 88 removed outlier: 4.118A pdb=" N GLU A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER A 86 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.662A pdb=" N SER A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.692A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 470 removed outlier: 3.816A pdb=" N GLU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.643A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 81 through 88 removed outlier: 4.149A pdb=" N GLU D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'D' and resid 381 through 402 removed outlier: 3.705A pdb=" N THR D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 470 removed outlier: 3.791A pdb=" N GLU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.672A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 81 through 88 removed outlier: 4.162A pdb=" N GLU G 85 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER G 86 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 88 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 201 through 209 Processing helix chain 'G' and resid 381 through 402 removed outlier: 3.694A pdb=" N THR G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 470 removed outlier: 3.805A pdb=" N GLU G 449 " --> pdb=" O LEU G 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 460 " --> pdb=" O ASP G 456 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 462 " --> pdb=" O ASN G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.653A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.719A pdb=" N GLU C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.682A pdb=" N GLU F 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.723A pdb=" N GLU I 84 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.591A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.582A pdb=" N SER A 127 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 272 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.582A pdb=" N SER A 127 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 272 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.751A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 303 removed outlier: 4.180A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.525A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.814A pdb=" N VAL B 110 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 380 Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.603A pdb=" N LEU D 67 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.595A pdb=" N SER D 127 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 272 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.595A pdb=" N SER D 127 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 272 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 150 through 155 removed outlier: 4.690A pdb=" N CYS D 153 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 178 through 183 Processing sheet with id=AC5, first strand: chain 'D' and resid 302 through 303 removed outlier: 4.184A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.632A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 92 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.632A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 92 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AD2, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AD3, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AD4, first strand: chain 'G' and resid 67 through 68 removed outlier: 6.584A pdb=" N LEU G 67 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE G 96 " --> pdb=" O ILE G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER G 127 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR G 270 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU G 193 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 272 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU G 193 " --> pdb=" O PRO G 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER G 127 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR G 270 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU G 193 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 272 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 150 through 155 removed outlier: 4.750A pdb=" N CYS G 153 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 178 through 183 Processing sheet with id=AD9, first strand: chain 'G' and resid 302 through 303 removed outlier: 4.187A pdb=" N CYS G 296 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.555A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.815A pdb=" N VAL H 110 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AE7, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.605A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.605A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.613A pdb=" N SER F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.607A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.607A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.623A pdb=" N SER I 71 " --> pdb=" O SER I 68 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1746 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: 2.89 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5376 1.35 - 1.47: 4297 1.47 - 1.58: 7349 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 17130 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 17125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 22885 1.78 - 3.56: 358 3.56 - 5.34: 36 5.34 - 7.12: 8 7.12 - 8.90: 4 Bond angle restraints: 23291 Sorted by residual: angle pdb=" C ASP C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C ASP F 51 " pdb=" N ASN F 52 " pdb=" CA ASN F 52 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.28e+00 angle pdb=" C TYR G 209 " pdb=" N GLN G 210 " pdb=" CA GLN G 210 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.20e+00 angle pdb=" C ASP I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.76e+00 angle pdb=" C CYS G 292 " pdb=" CA CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sigma weight residual 113.15 108.04 5.11 2.38e+00 1.77e-01 4.61e+00 ... (remaining 23286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 9339 21.55 - 43.09: 816 43.09 - 64.64: 166 64.64 - 86.18: 35 86.18 - 107.73: 15 Dihedral angle restraints: 10371 sinusoidal: 4234 harmonic: 6137 Sorted by residual: dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 292 " pdb=" CB CYS D 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.52 -65.48 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.83 -65.17 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual -86.00 -21.16 -64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 10368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2129 0.054 - 0.107: 397 0.107 - 0.161: 80 0.161 - 0.215: 0 0.215 - 0.268: 3 Chirality restraints: 2609 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2606 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 13 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO I 14 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 13 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO F 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 13 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.023 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1194 2.74 - 3.28: 14604 3.28 - 3.82: 25936 3.82 - 4.36: 31856 4.36 - 4.90: 58339 Nonbonded interactions: 131929 Sorted by model distance: nonbonded pdb=" OD2 ASP A 381 " pdb=" OG SER A 384 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP D 381 " pdb=" OG SER D 384 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP G 381 " pdb=" OG SER G 384 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS G 60 " pdb=" OD1 ASP G 291 " model vdw 2.222 3.120 nonbonded pdb=" NZ LYS A 60 " pdb=" OD1 ASP A 291 " model vdw 2.222 3.120 ... (remaining 131924 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 17 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 603)) selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'H' and (resid 2 through 29 or resid 31 through 119)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.032 17169 Z= 0.145 Angle : 0.562 8.904 23387 Z= 0.284 Chirality : 0.044 0.268 2609 Planarity : 0.004 0.044 2975 Dihedral : 16.979 107.725 6410 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.08 % Favored : 97.64 % Rotamer: Outliers : 3.52 % Allowed : 21.20 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2117 helix: 2.09 (0.29), residues: 351 sheet: 0.99 (0.21), residues: 579 loop : -0.79 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 234 TYR 0.012 0.001 TYR E 95 PHE 0.014 0.001 PHE A 128 TRP 0.009 0.001 TRP I 92 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00309 (17130) covalent geometry : angle 0.55530 (23291) SS BOND : bond 0.00257 ( 21) SS BOND : angle 1.48764 ( 42) hydrogen bonds : bond 0.15833 ( 620) hydrogen bonds : angle 6.05989 ( 1746) link_BETA1-4 : bond 0.00601 ( 6) link_BETA1-4 : angle 1.14092 ( 18) link_NAG-ASN : bond 0.00130 ( 12) link_NAG-ASN : angle 1.48996 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 0.668 Fit side-chains outliers start: 59 outliers final: 55 residues processed: 212 average time/residue: 0.5664 time to fit residues: 134.6126 Evaluate side-chains 204 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 173 ASN D 290 HIS D 469 GLN G 290 HIS I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100301 restraints weight = 19203.190| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.46 r_work: 0.3026 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17169 Z= 0.136 Angle : 0.558 9.469 23387 Z= 0.287 Chirality : 0.044 0.155 2609 Planarity : 0.004 0.037 2975 Dihedral : 9.293 65.172 2766 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.22 % Favored : 97.49 % Rotamer: Outliers : 4.25 % Allowed : 19.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2117 helix: 2.17 (0.29), residues: 357 sheet: 1.06 (0.21), residues: 597 loop : -0.72 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.016 0.001 TYR C 99 PHE 0.016 0.002 PHE G 128 TRP 0.011 0.001 TRP D 436 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00314 (17130) covalent geometry : angle 0.55123 (23291) SS BOND : bond 0.00259 ( 21) SS BOND : angle 1.27959 ( 42) hydrogen bonds : bond 0.06907 ( 620) hydrogen bonds : angle 4.59488 ( 1746) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 2.14942 ( 18) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.32800 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 0.584 Fit side-chains REVERT: A 374 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: A 494 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7012 (tp30) REVERT: B 30 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8085 (mtm-85) REVERT: D 188 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7607 (pttt) REVERT: D 222 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7542 (ttm170) REVERT: D 494 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7056 (tp30) REVERT: G 129 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: F 66 SER cc_start: 0.6888 (t) cc_final: 0.6399 (p) outliers start: 72 outliers final: 42 residues processed: 215 average time/residue: 0.5976 time to fit residues: 143.2393 Evaluate side-chains 198 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099385 restraints weight = 19481.418| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.49 r_work: 0.3010 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17169 Z= 0.146 Angle : 0.555 9.626 23387 Z= 0.285 Chirality : 0.044 0.167 2609 Planarity : 0.004 0.038 2975 Dihedral : 7.066 59.356 2733 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.46 % Favored : 97.26 % Rotamer: Outliers : 4.36 % Allowed : 19.80 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2117 helix: 2.20 (0.28), residues: 357 sheet: 1.16 (0.21), residues: 597 loop : -0.73 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 234 TYR 0.015 0.001 TYR H 95 PHE 0.018 0.002 PHE D 128 TRP 0.009 0.001 TRP D 436 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00348 (17130) covalent geometry : angle 0.54889 (23291) SS BOND : bond 0.00270 ( 21) SS BOND : angle 1.19695 ( 42) hydrogen bonds : bond 0.07108 ( 620) hydrogen bonds : angle 4.43464 ( 1746) link_BETA1-4 : bond 0.00604 ( 6) link_BETA1-4 : angle 1.86155 ( 18) link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.42396 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: A 494 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6944 (tp30) REVERT: B 30 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7387 (ptm-80) REVERT: D 172 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: D 188 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7770 (pttt) REVERT: D 222 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: D 494 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7030 (tp30) REVERT: G 129 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: G 172 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: G 188 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7647 (pttt) REVERT: G 373 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: G 374 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6586 (mt0) REVERT: F 32 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5464 (m-30) outliers start: 74 outliers final: 44 residues processed: 207 average time/residue: 0.6093 time to fit residues: 139.6953 Evaluate side-chains 181 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100102 restraints weight = 19314.654| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.46 r_work: 0.3023 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17169 Z= 0.131 Angle : 0.526 8.500 23387 Z= 0.271 Chirality : 0.044 0.162 2609 Planarity : 0.004 0.038 2975 Dihedral : 6.274 59.020 2729 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.41 % Favored : 97.30 % Rotamer: Outliers : 4.64 % Allowed : 19.24 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2117 helix: 2.32 (0.28), residues: 357 sheet: 1.18 (0.21), residues: 597 loop : -0.71 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 234 TYR 0.014 0.001 TYR H 95 PHE 0.017 0.002 PHE A 128 TRP 0.009 0.001 TRP D 436 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00304 (17130) covalent geometry : angle 0.52051 (23291) SS BOND : bond 0.00252 ( 21) SS BOND : angle 1.07073 ( 42) hydrogen bonds : bond 0.06777 ( 620) hydrogen bonds : angle 4.29954 ( 1746) link_BETA1-4 : bond 0.00512 ( 6) link_BETA1-4 : angle 1.63840 ( 18) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.39533 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 136 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: A 494 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6954 (tp30) REVERT: B 30 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6751 (ptm-80) REVERT: D 172 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: D 188 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (pttt) REVERT: D 222 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7544 (ttm170) REVERT: D 373 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: D 374 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6044 (mt0) REVERT: D 494 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7006 (tp30) REVERT: G 129 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: G 172 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: G 188 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7592 (pttt) REVERT: H 5 VAL cc_start: 0.7880 (t) cc_final: 0.7606 (m) REVERT: F 32 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5480 (m-30) REVERT: F 62 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5917 (ptm160) outliers start: 79 outliers final: 43 residues processed: 200 average time/residue: 0.6100 time to fit residues: 134.9696 Evaluate side-chains 184 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 366 TYR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 12 optimal weight: 0.0060 chunk 164 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102438 restraints weight = 19240.944| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.44 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17169 Z= 0.103 Angle : 0.483 8.185 23387 Z= 0.250 Chirality : 0.042 0.150 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.796 58.644 2725 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.27 % Favored : 97.45 % Rotamer: Outliers : 4.08 % Allowed : 19.52 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2117 helix: 2.52 (0.28), residues: 357 sheet: 1.30 (0.21), residues: 627 loop : -0.75 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.012 0.001 TYR H 95 PHE 0.014 0.001 PHE G 128 TRP 0.009 0.001 TRP G 436 HIS 0.003 0.000 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00214 (17130) covalent geometry : angle 0.47819 (23291) SS BOND : bond 0.00224 ( 21) SS BOND : angle 1.03000 ( 42) hydrogen bonds : bond 0.06096 ( 620) hydrogen bonds : angle 4.14499 ( 1746) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 1.39387 ( 18) link_NAG-ASN : bond 0.00178 ( 12) link_NAG-ASN : angle 1.27811 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 142 time to evaluate : 0.643 Fit side-chains REVERT: A 183 THR cc_start: 0.8096 (t) cc_final: 0.7709 (m) REVERT: A 374 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: A 494 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6968 (tp30) REVERT: B 30 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.6530 (ptm-80) REVERT: D 172 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: D 188 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7735 (pttt) REVERT: D 222 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: D 374 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6026 (mt0) REVERT: D 494 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6995 (tp30) REVERT: E 93 MET cc_start: 0.7476 (tpt) cc_final: 0.7227 (tpt) REVERT: G 129 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: G 172 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: G 188 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (pttt) REVERT: G 355 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: G 374 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6582 (mt0) REVERT: F 32 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5566 (m-30) REVERT: F 62 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5952 (ptm160) outliers start: 69 outliers final: 35 residues processed: 195 average time/residue: 0.6346 time to fit residues: 136.5889 Evaluate side-chains 185 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099265 restraints weight = 19330.311| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.50 r_work: 0.3003 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17169 Z= 0.158 Angle : 0.553 8.191 23387 Z= 0.284 Chirality : 0.044 0.168 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.858 57.545 2721 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.36 % Favored : 97.35 % Rotamer: Outliers : 4.25 % Allowed : 19.52 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2117 helix: 2.34 (0.28), residues: 357 sheet: 1.15 (0.21), residues: 603 loop : -0.75 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.016 0.001 TYR H 95 PHE 0.022 0.002 PHE A 128 TRP 0.008 0.001 TRP G 436 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00382 (17130) covalent geometry : angle 0.54686 (23291) SS BOND : bond 0.00283 ( 21) SS BOND : angle 1.05280 ( 42) hydrogen bonds : bond 0.07120 ( 620) hydrogen bonds : angle 4.29584 ( 1746) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.52722 ( 18) link_NAG-ASN : bond 0.00156 ( 12) link_NAG-ASN : angle 1.55192 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: A 494 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6976 (tp30) REVERT: B 30 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7604 (ptm-80) REVERT: D 172 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: D 188 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7807 (pttt) REVERT: D 222 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7600 (ttm170) REVERT: D 374 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6201 (mt0) REVERT: D 494 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6983 (tp30) REVERT: G 129 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: G 172 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: G 188 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7647 (pttt) REVERT: G 355 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: G 373 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: G 374 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6783 (mt0) REVERT: F 32 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5539 (m-30) REVERT: F 62 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6024 (ptm160) outliers start: 72 outliers final: 43 residues processed: 199 average time/residue: 0.6203 time to fit residues: 136.6540 Evaluate side-chains 190 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 141 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101501 restraints weight = 19196.989| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.45 r_work: 0.3039 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17169 Z= 0.107 Angle : 0.490 7.962 23387 Z= 0.254 Chirality : 0.043 0.157 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.616 57.698 2721 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.08 % Favored : 97.73 % Rotamer: Outliers : 4.03 % Allowed : 19.91 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2117 helix: 2.47 (0.28), residues: 357 sheet: 1.27 (0.21), residues: 627 loop : -0.77 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 234 TYR 0.012 0.001 TYR H 95 PHE 0.014 0.001 PHE A 128 TRP 0.009 0.001 TRP G 436 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00228 (17130) covalent geometry : angle 0.48478 (23291) SS BOND : bond 0.00222 ( 21) SS BOND : angle 1.00264 ( 42) hydrogen bonds : bond 0.06323 ( 620) hydrogen bonds : angle 4.17556 ( 1746) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 1.39212 ( 18) link_NAG-ASN : bond 0.00168 ( 12) link_NAG-ASN : angle 1.36664 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: A 494 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6948 (tp30) REVERT: B 30 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7546 (ptm-80) REVERT: D 172 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: D 188 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7774 (pttt) REVERT: D 222 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: D 374 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6115 (mt0) REVERT: D 494 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6971 (tp30) REVERT: G 129 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: G 172 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: G 188 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7556 (pttt) REVERT: G 355 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: G 374 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6660 (mt0) REVERT: H 5 VAL cc_start: 0.7870 (t) cc_final: 0.7597 (m) REVERT: F 32 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5520 (m-30) REVERT: F 62 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6007 (ptm160) outliers start: 68 outliers final: 40 residues processed: 194 average time/residue: 0.6259 time to fit residues: 134.2773 Evaluate side-chains 192 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 156 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098915 restraints weight = 19381.944| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.52 r_work: 0.2999 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17169 Z= 0.165 Angle : 0.556 7.834 23387 Z= 0.286 Chirality : 0.045 0.167 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.775 58.664 2721 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 3.86 % Allowed : 20.13 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2117 helix: 2.32 (0.28), residues: 357 sheet: 1.10 (0.21), residues: 603 loop : -0.79 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.016 0.001 TYR H 95 PHE 0.022 0.002 PHE A 128 TRP 0.008 0.001 TRP I 92 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00405 (17130) covalent geometry : angle 0.55045 (23291) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.05222 ( 42) hydrogen bonds : bond 0.07179 ( 620) hydrogen bonds : angle 4.30768 ( 1746) link_BETA1-4 : bond 0.00512 ( 6) link_BETA1-4 : angle 1.51483 ( 18) link_NAG-ASN : bond 0.00140 ( 12) link_NAG-ASN : angle 1.57823 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: A 494 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7013 (tp30) REVERT: B 30 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7685 (ptm-80) REVERT: B 48 MET cc_start: 0.8908 (mtp) cc_final: 0.8670 (mtp) REVERT: D 172 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: D 188 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7891 (pttt) REVERT: D 222 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7620 (ttm170) REVERT: D 374 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6310 (mt0) REVERT: D 494 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7041 (tp30) REVERT: G 129 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: G 172 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: G 188 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7716 (pttt) REVERT: G 373 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: H 5 VAL cc_start: 0.7932 (t) cc_final: 0.7655 (m) REVERT: F 62 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6082 (ptm160) REVERT: F 66 SER cc_start: 0.7300 (t) cc_final: 0.6811 (p) outliers start: 65 outliers final: 41 residues processed: 193 average time/residue: 0.6614 time to fit residues: 140.6067 Evaluate side-chains 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN D 486 HIS G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099014 restraints weight = 19318.889| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.50 r_work: 0.3002 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17169 Z= 0.159 Angle : 0.548 7.775 23387 Z= 0.283 Chirality : 0.045 0.171 2609 Planarity : 0.004 0.039 2975 Dihedral : 5.781 59.987 2721 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.41 % Favored : 97.45 % Rotamer: Outliers : 3.80 % Allowed : 20.36 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2117 helix: 2.26 (0.28), residues: 357 sheet: 1.12 (0.21), residues: 597 loop : -0.80 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.015 0.001 TYR H 95 PHE 0.020 0.002 PHE D 128 TRP 0.008 0.001 TRP I 92 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00388 (17130) covalent geometry : angle 0.54231 (23291) SS BOND : bond 0.00276 ( 21) SS BOND : angle 1.09289 ( 42) hydrogen bonds : bond 0.07171 ( 620) hydrogen bonds : angle 4.31930 ( 1746) link_BETA1-4 : bond 0.00501 ( 6) link_BETA1-4 : angle 1.50229 ( 18) link_NAG-ASN : bond 0.00142 ( 12) link_NAG-ASN : angle 1.58952 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: A 494 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6910 (tp30) REVERT: B 30 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7818 (ptm-80) REVERT: D 172 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: D 188 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7890 (pttt) REVERT: D 222 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: D 373 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: D 374 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6333 (mt0) REVERT: D 494 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7020 (tp30) REVERT: E 93 MET cc_start: 0.7571 (tpt) cc_final: 0.7334 (tpt) REVERT: G 129 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: G 172 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: G 188 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7705 (pttt) REVERT: G 373 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: H 5 VAL cc_start: 0.7913 (t) cc_final: 0.7646 (m) REVERT: F 62 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6125 (ptm160) REVERT: F 66 SER cc_start: 0.7346 (t) cc_final: 0.6862 (p) outliers start: 64 outliers final: 44 residues processed: 189 average time/residue: 0.6459 time to fit residues: 134.5710 Evaluate side-chains 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 88 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 182 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 HIS D 404 ASN D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101010 restraints weight = 19215.277| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.49 r_work: 0.3031 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17169 Z= 0.109 Angle : 0.493 7.453 23387 Z= 0.256 Chirality : 0.043 0.160 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.574 58.982 2721 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 3.36 % Allowed : 20.81 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2117 helix: 2.45 (0.28), residues: 357 sheet: 1.17 (0.21), residues: 612 loop : -0.71 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.012 0.001 TYR H 95 PHE 0.014 0.001 PHE G 128 TRP 0.009 0.001 TRP I 92 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00235 (17130) covalent geometry : angle 0.48737 (23291) SS BOND : bond 0.00228 ( 21) SS BOND : angle 1.00487 ( 42) hydrogen bonds : bond 0.06437 ( 620) hydrogen bonds : angle 4.20439 ( 1746) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 1.36359 ( 18) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.42415 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.8131 (t) cc_final: 0.7654 (m) REVERT: A 374 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: A 494 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6935 (tp30) REVERT: B 30 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7812 (ptm-80) REVERT: D 172 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: D 188 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7845 (pttt) REVERT: D 222 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: D 373 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: D 374 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6197 (mt0) REVERT: D 494 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7000 (tp30) REVERT: E 93 MET cc_start: 0.7448 (tpt) cc_final: 0.7222 (tpt) REVERT: G 129 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: G 172 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: G 188 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7595 (pttt) REVERT: G 373 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: H 5 VAL cc_start: 0.7848 (t) cc_final: 0.7581 (m) REVERT: F 62 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6081 (ptm160) REVERT: F 66 SER cc_start: 0.7426 (t) cc_final: 0.6979 (p) outliers start: 56 outliers final: 40 residues processed: 197 average time/residue: 0.6296 time to fit residues: 137.2272 Evaluate side-chains 199 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098757 restraints weight = 19228.015| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.49 r_work: 0.2996 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17169 Z= 0.176 Angle : 0.569 7.262 23387 Z= 0.293 Chirality : 0.045 0.170 2609 Planarity : 0.004 0.039 2975 Dihedral : 5.739 58.572 2721 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.51 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 20.92 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2117 helix: 2.30 (0.28), residues: 357 sheet: 1.08 (0.21), residues: 603 loop : -0.83 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.016 0.001 TYR H 95 PHE 0.022 0.002 PHE A 128 TRP 0.009 0.001 TRP C 36 HIS 0.006 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00434 (17130) covalent geometry : angle 0.56354 (23291) SS BOND : bond 0.00308 ( 21) SS BOND : angle 1.06699 ( 42) hydrogen bonds : bond 0.07307 ( 620) hydrogen bonds : angle 4.31793 ( 1746) link_BETA1-4 : bond 0.00531 ( 6) link_BETA1-4 : angle 1.53275 ( 18) link_NAG-ASN : bond 0.00127 ( 12) link_NAG-ASN : angle 1.62632 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.63 seconds wall clock time: 128 minutes 44.30 seconds (7724.30 seconds total)