Starting phenix.real_space_refine on Sun Jul 5 18:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dim_27440/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_2026/8dim_27440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dim_27440/07_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-6108/lib/python3.11/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 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 chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 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: 3.89, per 1000 atoms: 0.23 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: 1.56 Conformation dependent library (CDL) restraints added in 849.3 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: 0.78 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: 3.31 Time building geometry restraints manager: 2.07 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 - 17.65: 8687 17.65 - 35.30: 952 35.30 - 52.95: 289 52.95 - 70.60: 62 70.60 - 88.25: 9 Dihedral angle restraints: 9999 sinusoidal: 3862 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 9996 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: 18.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 16.178 88.250 6038 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/Z covalent geometry : bond 0.00309 / 0.15 (17130) covalent geometry : angle 0.55530 / 0.28 (23291) SS BOND : bond 0.00257 / 0.16 ( 21) SS BOND : angle 1.48764 / 0.84 ( 42) hydrogen bonds : bond 0.15833 / 10.72 ( 620) hydrogen bonds : angle 6.05989 / 4.20 ( 1746) link_BETA1-4 : bond 0.00601 / 0.34 ( 6) link_BETA1-4 : angle 1.14092 / 0.63 ( 18) link_NAG-ASN : bond 0.00130 / 0.09 ( 12) link_NAG-ASN : angle 1.48996 / 0.98 ( 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 : 0.670 Fit side-chains outliers start: 59 outliers final: 55 residues processed: 212 average time/residue: 0.5637 time to fit residues: 134.6810 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 : 0.632 ------------------------------------------------------------------------------- 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... 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 = 0.142648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100350 restraints weight = 19205.849| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.46 r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 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 = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0502 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 : 0.551 9.468 23387 Z= 0.286 Chirality : 0.044 0.155 2609 Planarity : 0.004 0.037 2975 Dihedral : 7.272 59.286 2394 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.27 % Favored : 97.45 % Rotamer: Outliers : 4.31 % Allowed : 19.63 % 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 0.003 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/Z covalent geometry : bond 0.00315 / 0.14 (17130) covalent geometry : angle 0.54549 / 0.28 (23291) SS BOND : bond 0.00262 / 0.16 ( 21) SS BOND : angle 1.27532 / 0.73 ( 42) hydrogen bonds : bond 0.06899 / 4.59 ( 620) hydrogen bonds : angle 4.59758 / 3.20 ( 1746) link_BETA1-4 : bond 0.00445 / 0.23 ( 6) link_BETA1-4 : angle 1.56884 / 0.87 ( 18) link_NAG-ASN : bond 0.00170 / 0.10 ( 12) link_NAG-ASN : angle 1.31114 / 0.84 ( 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 234 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 0.675 Fit side-chains REVERT: A 374 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: A 494 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7004 (tp30) REVERT: B 30 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8119 (mtm-85) REVERT: D 188 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7586 (pttt) REVERT: D 222 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: D 494 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7049 (tp30) REVERT: G 129 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: G 355 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: F 66 SER cc_start: 0.6905 (t) cc_final: 0.6416 (p) outliers start: 73 outliers final: 43 residues processed: 216 average time/residue: 0.6079 time to fit residues: 146.8943 Evaluate side-chains 200 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 278 SER Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 355 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 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: 2.9990 chunk 166 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3734 r_free = 0.3734 target = 0.140401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097732 restraints weight = 19484.558| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.57 r_work: 0.2988 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17169 Z= 0.183 Angle : 0.595 9.673 23387 Z= 0.306 Chirality : 0.045 0.178 2609 Planarity : 0.005 0.041 2975 Dihedral : 6.714 59.897 2362 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.55 % Favored : 97.16 % Rotamer: Outliers : 4.81 % Allowed : 19.24 % Favored : 75.95 % 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: 0.41 (0.18), residues: 2117 helix: 2.05 (0.28), residues: 357 sheet: 1.12 (0.21), residues: 597 loop : -0.79 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.016 0.002 TYR H 95 PHE 0.022 0.002 PHE A 128 TRP 0.011 0.001 TRP C 92 HIS 0.006 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.18 (17130) covalent geometry : angle 0.58903 / 0.30 (23291) SS BOND : bond 0.00304 / 0.19 ( 21) SS BOND : angle 1.20301 / 0.69 ( 42) hydrogen bonds : bond 0.07697 / 5.13 ( 620) hydrogen bonds : angle 4.55155 / 3.17 ( 1746) link_BETA1-4 : bond 0.00528 / 0.28 ( 6) link_BETA1-4 : angle 1.36130 / 0.77 ( 18) link_NAG-ASN : bond 0.00151 / 0.09 ( 12) link_NAG-ASN : angle 1.60133 / 1.06 ( 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 231 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 149 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: A 494 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6926 (tp30) REVERT: B 30 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7301 (ptm-80) REVERT: D 172 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: D 188 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7798 (pttt) REVERT: D 222 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7569 (ttm170) REVERT: D 494 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7014 (tp30) REVERT: G 129 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: G 172 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: G 188 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7704 (pttt) REVERT: G 310 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: G 373 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: G 374 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: F 32 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.5447 (m-30) REVERT: F 62 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5880 (ptm160) outliers start: 82 outliers final: 47 residues processed: 215 average time/residue: 0.6281 time to fit residues: 150.5993 Evaluate side-chains 187 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 31 SER 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 327 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR 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 267 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 335 LEU 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: 0.4980 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3764 r_free = 0.3764 target = 0.142898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100874 restraints weight = 19322.773| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.44 r_work: 0.3033 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 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 = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17169 Z= 0.112 Angle : 0.503 9.148 23387 Z= 0.261 Chirality : 0.043 0.158 2609 Planarity : 0.004 0.038 2975 Dihedral : 6.274 59.228 2359 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.13 % Favored : 97.59 % Rotamer: Outliers : 4.31 % Allowed : 19.41 % Favored : 76.29 % 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: 0.58 (0.18), residues: 2117 helix: 2.31 (0.28), residues: 357 sheet: 1.27 (0.21), residues: 627 loop : -0.81 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.012 0.001 TYR H 95 PHE 0.013 0.001 PHE G 128 TRP 0.009 0.001 TRP C 92 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17130) covalent geometry : angle 0.49779 / 0.26 (23291) SS BOND : bond 0.00232 / 0.14 ( 21) SS BOND : angle 1.07610 / 0.62 ( 42) hydrogen bonds : bond 0.06505 / 4.33 ( 620) hydrogen bonds : angle 4.28114 / 2.98 ( 1746) link_BETA1-4 : bond 0.00445 / 0.24 ( 6) link_BETA1-4 : angle 1.23059 / 0.68 ( 18) link_NAG-ASN : bond 0.00139 / 0.08 ( 12) link_NAG-ASN : angle 1.31373 / 0.86 ( 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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 139 time to evaluate : 0.616 Fit side-chains REVERT: A 374 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: A 494 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6934 (tp30) REVERT: B 30 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6774 (ptm-80) REVERT: D 172 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: D 188 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7754 (pttt) REVERT: D 222 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7523 (ttm170) REVERT: D 373 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: D 374 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.5996 (mt0) REVERT: D 494 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6991 (tp30) REVERT: G 129 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: G 172 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: G 188 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7560 (pttt) REVERT: H 5 VAL cc_start: 0.7857 (t) cc_final: 0.7590 (m) REVERT: F 32 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: F 62 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.5946 (ptm160) outliers start: 73 outliers final: 36 residues processed: 198 average time/residue: 0.6647 time to fit residues: 145.8733 Evaluate side-chains 182 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS 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 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 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 292 CYS 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 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: 4.9990 chunk 85 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099597 restraints weight = 19260.360| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.43 r_work: 0.3010 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 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 = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0915 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= 0.143 Angle : 0.539 8.491 23387 Z= 0.278 Chirality : 0.044 0.166 2609 Planarity : 0.004 0.042 2975 Dihedral : 6.194 59.381 2353 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.41 % Favored : 97.30 % Rotamer: Outliers : 4.47 % Allowed : 19.18 % Favored : 76.34 % 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: 0.56 (0.18), residues: 2117 helix: 2.32 (0.28), residues: 357 sheet: 1.19 (0.21), residues: 597 loop : -0.74 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 467 TYR 0.014 0.001 TYR H 95 PHE 0.019 0.002 PHE G 128 TRP 0.010 0.001 TRP C 92 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (17130) covalent geometry : angle 0.53375 / 0.28 (23291) SS BOND : bond 0.00270 / 0.17 ( 21) SS BOND : angle 1.09562 / 0.63 ( 42) hydrogen bonds : bond 0.06951 / 4.63 ( 620) hydrogen bonds : angle 4.31249 / 3.00 ( 1746) link_BETA1-4 : bond 0.00456 / 0.24 ( 6) link_BETA1-4 : angle 1.24004 / 0.69 ( 18) link_NAG-ASN : bond 0.00119 / 0.07 ( 12) link_NAG-ASN : angle 1.46872 / 0.96 ( 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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: A 494 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6929 (tp30) REVERT: B 30 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.6579 (ptm-80) REVERT: D 172 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 188 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7764 (pttt) REVERT: D 222 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: D 373 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: D 374 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6130 (mt0) REVERT: D 494 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6948 (tp30) REVERT: G 129 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: G 172 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: G 188 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7610 (pttt) REVERT: G 374 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6670 (mt0) REVERT: H 5 VAL cc_start: 0.7874 (t) cc_final: 0.7595 (m) REVERT: F 32 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5509 (m-30) REVERT: F 62 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6247 (ptm-80) outliers start: 76 outliers final: 41 residues processed: 197 average time/residue: 0.6043 time to fit residues: 132.3500 Evaluate side-chains 184 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 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 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 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 292 CYS 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 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 73 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: 2.9990 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093049 restraints weight = 19339.185| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.43 r_work: 0.3017 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17169 Z= 0.178 Angle : 0.572 8.579 23387 Z= 0.294 Chirality : 0.045 0.177 2609 Planarity : 0.004 0.040 2975 Dihedral : 6.288 58.676 2353 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.36 % Favored : 97.40 % Rotamer: Outliers : 4.08 % Allowed : 19.46 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2117 helix: 2.21 (0.28), residues: 357 sheet: 1.11 (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 G 467 TYR 0.016 0.001 TYR H 95 PHE 0.021 0.002 PHE A 128 TRP 0.009 0.001 TRP C 92 HIS 0.006 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (17130) covalent geometry : angle 0.56676 / 0.29 (23291) SS BOND : bond 0.00304 / 0.19 ( 21) SS BOND : angle 1.13757 / 0.66 ( 42) hydrogen bonds : bond 0.07408 / 4.93 ( 620) hydrogen bonds : angle 4.39505 / 3.06 ( 1746) link_BETA1-4 : bond 0.00392 / 0.21 ( 6) link_BETA1-4 : angle 1.28132 / 0.72 ( 18) link_NAG-ASN : bond 0.00118 / 0.07 ( 12) link_NAG-ASN : angle 1.61637 / 1.07 ( 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 201 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: A 494 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6928 (tp30) REVERT: B 30 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7691 (ptm-80) REVERT: D 172 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: D 188 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7791 (pttt) REVERT: D 222 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7548 (ttm170) REVERT: D 373 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: D 374 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6258 (mt0) REVERT: D 494 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6961 (tp30) REVERT: G 129 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: G 172 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: G 188 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7662 (pttt) REVERT: G 373 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: G 374 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: H 5 VAL cc_start: 0.7873 (t) cc_final: 0.7605 (m) REVERT: F 62 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6210 (ptm-80) outliers start: 69 outliers final: 44 residues processed: 191 average time/residue: 0.6410 time to fit residues: 136.1233 Evaluate side-chains 186 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 90 optimal weight: 0.7980 chunk 192 optimal weight: 0.0570 chunk 196 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 191 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.0670 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 39 GLN 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 = 0.3782 r_free = 0.3782 target = 0.144388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097553 restraints weight = 19204.004| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.43 r_work: 0.3081 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1046 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= 0.096 Angle : 0.471 8.122 23387 Z= 0.245 Chirality : 0.042 0.150 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.904 57.647 2353 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.08 % Favored : 97.73 % Rotamer: Outliers : 3.58 % Allowed : 20.58 % 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: 0.69 (0.18), residues: 2117 helix: 2.53 (0.28), residues: 357 sheet: 1.29 (0.21), residues: 627 loop : -0.76 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.010 0.001 TYR H 95 PHE 0.010 0.001 PHE A 128 TRP 0.010 0.001 TRP C 92 HIS 0.002 0.000 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.10 (17130) covalent geometry : angle 0.46654 / 0.24 (23291) SS BOND : bond 0.00213 / 0.13 ( 21) SS BOND : angle 1.00859 / 0.58 ( 42) hydrogen bonds : bond 0.05964 / 3.97 ( 620) hydrogen bonds : angle 4.14711 / 2.88 ( 1746) link_BETA1-4 : bond 0.00502 / 0.27 ( 6) link_BETA1-4 : angle 1.16942 / 0.65 ( 18) link_NAG-ASN : bond 0.00150 / 0.09 ( 12) link_NAG-ASN : angle 1.23788 / 0.80 ( 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 209 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.657 Fit side-chains REVERT: A 183 THR cc_start: 0.8064 (t) cc_final: 0.7683 (m) REVERT: A 374 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: A 494 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6928 (tp30) REVERT: B 30 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7577 (ptm-80) REVERT: D 172 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: D 188 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7750 (pttt) REVERT: D 222 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: D 374 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6086 (mt0) REVERT: D 494 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6981 (tp30) REVERT: G 129 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: G 172 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: G 188 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7558 (pttt) REVERT: G 355 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: G 373 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: G 374 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6731 (mt0) REVERT: H 5 VAL cc_start: 0.7835 (t) cc_final: 0.7570 (m) REVERT: F 32 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5553 (m-30) REVERT: F 62 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6194 (ptm-80) REVERT: F 66 SER cc_start: 0.7143 (t) cc_final: 0.6667 (p) outliers start: 60 outliers final: 27 residues processed: 194 average time/residue: 0.6402 time to fit residues: 137.3319 Evaluate side-chains 183 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 331 MET Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain E residue 20 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 129 optimal weight: 0.0170 chunk 177 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 GLN D 290 HIS D 469 GLN G 290 HIS F 39 GLN 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 = 0.3762 r_free = 0.3762 target = 0.142640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100658 restraints weight = 19381.509| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.43 r_work: 0.3029 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 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 = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17169 Z= 0.125 Angle : 0.509 7.647 23387 Z= 0.263 Chirality : 0.043 0.159 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.848 58.640 2349 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.41 % Favored : 97.45 % Rotamer: Outliers : 3.52 % Allowed : 20.75 % Favored : 75.73 % 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: 0.65 (0.18), residues: 2117 helix: 2.53 (0.28), residues: 357 sheet: 1.25 (0.21), residues: 627 loop : -0.78 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 467 TYR 0.013 0.001 TYR H 95 PHE 0.018 0.002 PHE A 128 TRP 0.008 0.001 TRP I 92 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17130) covalent geometry : angle 0.50411 / 0.26 (23291) SS BOND : bond 0.00256 / 0.16 ( 21) SS BOND : angle 1.00433 / 0.58 ( 42) hydrogen bonds : bond 0.06478 / 4.31 ( 620) hydrogen bonds : angle 4.17701 / 2.91 ( 1746) link_BETA1-4 : bond 0.00448 / 0.23 ( 6) link_BETA1-4 : angle 1.21577 / 0.68 ( 18) link_NAG-ASN : bond 0.00120 / 0.07 ( 12) link_NAG-ASN : angle 1.37740 / 0.90 ( 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 205 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 494 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6957 (tp30) REVERT: B 30 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7553 (ptm-80) REVERT: D 172 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: D 188 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7764 (pttt) REVERT: D 222 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: D 374 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6097 (mt0) REVERT: D 494 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6990 (tp30) REVERT: G 129 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: G 172 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: G 188 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7594 (pttt) REVERT: G 373 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: G 374 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6734 (mt0) REVERT: H 5 VAL cc_start: 0.7886 (t) cc_final: 0.7611 (m) REVERT: F 62 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6044 (ptm160) REVERT: F 66 SER cc_start: 0.7244 (t) cc_final: 0.6757 (p) outliers start: 59 outliers final: 37 residues processed: 194 average time/residue: 0.6378 time to fit residues: 137.4051 Evaluate side-chains 191 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 29 SER 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 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 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 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=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: 0.6980 chunk 47 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 39 GLN 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 = 0.3764 r_free = 0.3764 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101167 restraints weight = 19366.399| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.45 r_work: 0.3033 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 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 = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17169 Z= 0.120 Angle : 0.503 7.581 23387 Z= 0.260 Chirality : 0.043 0.159 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.816 59.030 2349 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.51 % Favored : 97.35 % Rotamer: Outliers : 3.30 % Allowed : 20.81 % Favored : 75.89 % 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: 0.65 (0.18), residues: 2117 helix: 2.53 (0.28), residues: 357 sheet: 1.23 (0.20), residues: 642 loop : -0.79 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 467 TYR 0.013 0.001 TYR H 95 PHE 0.016 0.001 PHE A 128 TRP 0.010 0.001 TRP C 92 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17130) covalent geometry : angle 0.49827 / 0.26 (23291) SS BOND : bond 0.00255 / 0.16 ( 21) SS BOND : angle 1.03008 / 0.60 ( 42) hydrogen bonds : bond 0.06424 / 4.28 ( 620) hydrogen bonds : angle 4.17789 / 2.91 ( 1746) link_BETA1-4 : bond 0.00464 / 0.25 ( 6) link_BETA1-4 : angle 1.19250 / 0.67 ( 18) link_NAG-ASN : bond 0.00122 / 0.07 ( 12) link_NAG-ASN : angle 1.37317 / 0.89 ( 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 199 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.8156 (t) cc_final: 0.7682 (m) REVERT: A 374 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: A 494 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6969 (tp30) REVERT: B 30 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7559 (ptm-80) REVERT: D 172 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: D 188 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7766 (pttt) REVERT: D 222 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: D 374 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6109 (mt0) REVERT: D 494 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6991 (tp30) REVERT: G 129 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: G 172 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: G 188 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7585 (pttt) REVERT: G 373 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: G 374 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6757 (mt0) REVERT: H 5 VAL cc_start: 0.7896 (t) cc_final: 0.7621 (m) REVERT: F 62 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6037 (ptm160) REVERT: F 66 SER cc_start: 0.7242 (t) cc_final: 0.6775 (p) outliers start: 55 outliers final: 37 residues processed: 191 average time/residue: 0.6427 time to fit residues: 136.5753 Evaluate side-chains 192 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS 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 29 SER 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 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 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 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 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: 4.9990 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 39 GLN F 52 ASN I 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093342 restraints weight = 19275.370| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.48 r_work: 0.3020 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17169 Z= 0.162 Angle : 0.559 7.570 23387 Z= 0.288 Chirality : 0.045 0.176 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.982 59.854 2349 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.12 % Rotamer: Outliers : 3.41 % Allowed : 20.86 % Favored : 75.73 % 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: 0.50 (0.18), residues: 2117 helix: 2.33 (0.28), residues: 357 sheet: 1.13 (0.21), residues: 603 loop : -0.79 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 467 TYR 0.015 0.001 TYR B 95 PHE 0.021 0.002 PHE A 128 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (17130) covalent geometry : angle 0.55301 / 0.29 (23291) SS BOND : bond 0.00299 / 0.19 ( 21) SS BOND : angle 1.10079 / 0.64 ( 42) hydrogen bonds : bond 0.07223 / 4.81 ( 620) hydrogen bonds : angle 4.31854 / 3.01 ( 1746) link_BETA1-4 : bond 0.00480 / 0.25 ( 6) link_BETA1-4 : angle 1.25662 / 0.71 ( 18) link_NAG-ASN : bond 0.00118 / 0.07 ( 12) link_NAG-ASN : angle 1.61768 / 1.06 ( 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 203 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: A 494 GLU cc_start: 0.7434 (mm-30) cc_final: 0.6831 (tp30) REVERT: B 30 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7686 (ptm-80) REVERT: D 172 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: D 188 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7769 (pttt) REVERT: D 222 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7533 (ttm170) REVERT: D 374 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6217 (mt0) REVERT: D 494 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6917 (tp30) REVERT: G 129 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: G 172 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: G 188 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7605 (pttt) REVERT: G 373 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: H 5 VAL cc_start: 0.7854 (t) cc_final: 0.7579 (m) REVERT: H 93 MET cc_start: 0.7719 (tpt) cc_final: 0.7478 (tpp) REVERT: F 62 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6026 (ptm160) REVERT: F 66 SER cc_start: 0.7269 (t) cc_final: 0.6791 (p) outliers start: 57 outliers final: 37 residues processed: 193 average time/residue: 0.6044 time to fit residues: 129.5567 Evaluate side-chains 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 39 GLN ** 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 = 0.3743 r_free = 0.3743 target = 0.140951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098882 restraints weight = 19261.567| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.45 r_work: 0.3002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 17169 Z= 0.174 Angle : 0.770 59.195 23387 Z= 0.434 Chirality : 0.044 0.177 2609 Planarity : 0.004 0.038 2975 Dihedral : 6.019 59.865 2349 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 3.24 % Allowed : 21.31 % Favored : 75.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2117 helix: 2.32 (0.28), residues: 357 sheet: 1.12 (0.21), residues: 603 loop : -0.80 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 467 TYR 0.015 0.001 TYR B 95 PHE 0.020 0.002 PHE A 128 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (17130) covalent geometry : angle 0.76648 / 0.43 (23291) SS BOND : bond 0.00296 / 0.18 ( 21) SS BOND : angle 1.09974 / 0.64 ( 42) hydrogen bonds : bond 0.07205 / 4.80 ( 620) hydrogen bonds : angle 4.31775 / 3.01 ( 1746) link_BETA1-4 : bond 0.00357 / 0.19 ( 6) link_BETA1-4 : angle 1.28623 / 0.73 ( 18) link_NAG-ASN : bond 0.00119 / 0.07 ( 12) link_NAG-ASN : angle 1.61635 / 1.06 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7415.13 seconds wall clock time: 126 minutes 45.97 seconds (7605.97 seconds total)