Starting phenix.real_space_refine on Tue May 27 18:03:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_27440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_27440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_27440.map" model { file = "/net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_27440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dim_27440/05_2025/8dim_27440.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 903 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.55, per 1000 atoms: 0.63 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: 4.14 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.63 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: 5.94 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5376 1.35 - 1.47: 4297 1.47 - 1.58: 7349 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 17130 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 17125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 22885 1.78 - 3.56: 358 3.56 - 5.34: 36 5.34 - 7.12: 8 7.12 - 8.90: 4 Bond angle restraints: 23291 Sorted by residual: angle pdb=" C ASP C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C ASP F 51 " pdb=" N ASN F 52 " pdb=" CA ASN F 52 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.28e+00 angle pdb=" C TYR G 209 " pdb=" N GLN G 210 " pdb=" CA GLN G 210 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.20e+00 angle pdb=" C ASP I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.76e+00 angle pdb=" C CYS G 292 " pdb=" CA CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sigma weight residual 113.15 108.04 5.11 2.38e+00 1.77e-01 4.61e+00 ... (remaining 23286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 9339 21.55 - 43.09: 816 43.09 - 64.64: 166 64.64 - 86.18: 35 86.18 - 107.73: 15 Dihedral angle restraints: 10371 sinusoidal: 4234 harmonic: 6137 Sorted by residual: dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 292 " pdb=" CB CYS D 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.52 -65.48 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.83 -65.17 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual -86.00 -21.16 -64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 10368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2129 0.054 - 0.107: 397 0.107 - 0.161: 80 0.161 - 0.215: 0 0.215 - 0.268: 3 Chirality restraints: 2609 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2606 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 13 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO I 14 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 13 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO F 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 13 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.023 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1194 2.74 - 3.28: 14604 3.28 - 3.82: 25936 3.82 - 4.36: 31856 4.36 - 4.90: 58339 Nonbonded interactions: 131929 Sorted by model distance: nonbonded pdb=" OD2 ASP A 381 " pdb=" OG SER A 384 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP D 381 " pdb=" OG SER D 384 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP G 381 " pdb=" OG SER G 384 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS G 60 " pdb=" OD1 ASP G 291 " model vdw 2.222 3.120 nonbonded pdb=" NZ LYS A 60 " pdb=" OD1 ASP A 291 " model vdw 2.222 3.120 ... (remaining 131924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 506 or resid 601 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: 14.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 42.820 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17169 Z= 0.145 Angle : 0.562 8.904 23387 Z= 0.284 Chirality : 0.044 0.268 2609 Planarity : 0.004 0.044 2975 Dihedral : 16.979 107.725 6410 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (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 TRP 0.009 0.001 TRP I 92 HIS 0.004 0.001 HIS A 25 PHE 0.014 0.001 PHE A 128 TYR 0.012 0.001 TYR E 95 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 12) link_NAG-ASN : angle 1.48996 ( 36) link_BETA1-4 : bond 0.00601 ( 6) link_BETA1-4 : angle 1.14092 ( 18) hydrogen bonds : bond 0.15833 ( 620) hydrogen bonds : angle 6.05989 ( 1746) SS BOND : bond 0.00257 ( 21) SS BOND : angle 1.48764 ( 42) covalent geometry : bond 0.00309 (17130) covalent geometry : angle 0.55530 (23291) *********************** 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 : 1.922 Fit side-chains outliers start: 59 outliers final: 55 residues processed: 212 average time/residue: 1.1534 time to fit residues: 275.1428 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 : 1.711 ------------------------------------------------------------------------------- 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 174 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 173 ASN D 290 HIS D 469 GLN G 290 HIS I 39 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.140774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098271 restraints weight = 19148.749| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.47 r_work: 0.2996 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 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 = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17169 Z= 0.179 Angle : 0.610 9.594 23387 Z= 0.312 Chirality : 0.046 0.175 2609 Planarity : 0.005 0.039 2975 Dihedral : 9.134 60.596 2766 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.36 % Favored : 97.35 % Rotamer: Outliers : 4.47 % Allowed : 20.08 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2117 helix: 1.96 (0.28), residues: 357 sheet: 1.02 (0.21), residues: 597 loop : -0.80 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.006 0.001 HIS A 25 PHE 0.020 0.002 PHE G 128 TYR 0.016 0.002 TYR C 99 ARG 0.004 0.000 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 12) link_NAG-ASN : angle 1.46083 ( 36) link_BETA1-4 : bond 0.00421 ( 6) link_BETA1-4 : angle 2.25369 ( 18) hydrogen bonds : bond 0.07585 ( 620) hydrogen bonds : angle 4.69378 ( 1746) SS BOND : bond 0.00305 ( 21) SS BOND : angle 1.34545 ( 42) covalent geometry : bond 0.00439 (17130) covalent geometry : angle 0.60228 (23291) *********************** 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 231 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 155 time to evaluate : 1.739 Fit side-chains REVERT: A 374 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: A 494 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7001 (tp30) REVERT: B 30 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8329 (mtm-85) REVERT: D 188 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7702 (pttt) REVERT: D 222 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: D 494 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7035 (tp30) REVERT: G 129 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: F 32 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5451 (m-30) REVERT: F 66 SER cc_start: 0.6941 (t) cc_final: 0.6445 (p) outliers start: 76 outliers final: 44 residues processed: 213 average time/residue: 1.2599 time to fit residues: 300.0014 Evaluate side-chains 185 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 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 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 E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 43 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 77 optimal weight: 0.0020 chunk 182 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100817 restraints weight = 19167.664| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.44 r_work: 0.3031 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17169 Z= 0.119 Angle : 0.518 9.714 23387 Z= 0.267 Chirality : 0.043 0.159 2609 Planarity : 0.004 0.037 2975 Dihedral : 6.884 59.770 2733 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.99 % Favored : 97.73 % Rotamer: Outliers : 4.03 % Allowed : 19.91 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2117 helix: 2.26 (0.28), residues: 357 sheet: 1.28 (0.21), residues: 579 loop : -0.72 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.004 0.001 HIS A 25 PHE 0.015 0.001 PHE D 128 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 12) link_NAG-ASN : angle 1.30260 ( 36) link_BETA1-4 : bond 0.00633 ( 6) link_BETA1-4 : angle 1.77331 ( 18) hydrogen bonds : bond 0.06645 ( 620) hydrogen bonds : angle 4.36681 ( 1746) SS BOND : bond 0.00245 ( 21) SS BOND : angle 1.16595 ( 42) covalent geometry : bond 0.00264 (17130) covalent geometry : angle 0.51186 (23291) *********************** 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 218 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 150 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: A 494 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6929 (tp30) REVERT: B 30 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7479 (ptm-80) REVERT: D 172 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 188 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7748 (pttt) REVERT: D 222 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: D 494 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6988 (tp30) REVERT: G 129 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: G 172 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: G 188 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7531 (pttt) REVERT: G 373 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: G 374 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6500 (mt0) REVERT: F 62 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6275 (ptm-80) outliers start: 68 outliers final: 39 residues processed: 205 average time/residue: 1.2660 time to fit residues: 288.7714 Evaluate side-chains 180 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain 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 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 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 305 THR Chi-restraints excluded: chain G residue 366 TYR 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 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 44 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3753 r_free = 0.3753 target = 0.141926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094534 restraints weight = 19245.954| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.44 r_work: 0.3038 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 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 = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0840 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= 0.136 Angle : 0.535 8.607 23387 Z= 0.275 Chirality : 0.044 0.161 2609 Planarity : 0.004 0.037 2975 Dihedral : 6.301 59.628 2729 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.55 % Favored : 97.16 % Rotamer: Outliers : 4.59 % Allowed : 18.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2117 helix: 2.30 (0.28), residues: 357 sheet: 1.19 (0.21), residues: 597 loop : -0.71 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS A 25 PHE 0.018 0.002 PHE D 128 TYR 0.014 0.001 TYR H 95 ARG 0.004 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.40905 ( 36) link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 1.65518 ( 18) hydrogen bonds : bond 0.06855 ( 620) hydrogen bonds : angle 4.31835 ( 1746) SS BOND : bond 0.00259 ( 21) SS BOND : angle 1.07631 ( 42) covalent geometry : bond 0.00320 (17130) covalent geometry : angle 0.52926 (23291) *********************** 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 213 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 135 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: A 494 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6915 (tp30) REVERT: B 30 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.6822 (ptm-80) REVERT: D 172 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 188 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7736 (pttt) REVERT: D 222 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7548 (ttm170) REVERT: D 373 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: D 374 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: D 494 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6952 (tp30) REVERT: G 129 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: G 172 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: G 188 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7572 (pttt) REVERT: G 374 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6569 (mt0) REVERT: F 32 ASP cc_start: 0.5912 (OUTLIER) cc_final: 0.5486 (m-30) REVERT: F 62 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.5929 (ptm160) outliers start: 78 outliers final: 41 residues processed: 198 average time/residue: 1.3197 time to fit residues: 290.7426 Evaluate side-chains 183 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 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 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 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 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 chunk 197 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3764 r_free = 0.3764 target = 0.142738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100747 restraints weight = 19499.405| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.50 r_work: 0.3031 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 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 = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17169 Z= 0.120 Angle : 0.509 8.237 23387 Z= 0.263 Chirality : 0.043 0.157 2609 Planarity : 0.004 0.048 2975 Dihedral : 5.947 58.321 2725 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.17 % Favored : 97.54 % Rotamer: Outliers : 4.47 % Allowed : 19.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2117 helix: 2.39 (0.28), residues: 357 sheet: 1.23 (0.21), residues: 597 loop : -0.69 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS A 25 PHE 0.016 0.001 PHE A 128 TYR 0.013 0.001 TYR B 95 ARG 0.002 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 12) link_NAG-ASN : angle 1.36782 ( 36) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 1.46512 ( 18) hydrogen bonds : bond 0.06543 ( 620) hydrogen bonds : angle 4.22574 ( 1746) SS BOND : bond 0.00247 ( 21) SS BOND : angle 1.07481 ( 42) covalent geometry : bond 0.00271 (17130) covalent geometry : angle 0.50315 (23291) *********************** 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 216 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 140 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: A 406 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.5888 (mt0) REVERT: A 494 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6986 (tp30) REVERT: B 30 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.6589 (ptm-80) REVERT: D 172 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: D 188 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7806 (pttt) REVERT: D 222 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: D 373 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: D 374 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6135 (mt0) REVERT: D 494 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7003 (tp30) REVERT: G 129 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: G 172 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: G 188 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7606 (pttt) REVERT: G 355 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: F 32 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5578 (m-30) REVERT: F 62 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5972 (ptm160) outliers start: 76 outliers final: 44 residues processed: 200 average time/residue: 1.2995 time to fit residues: 288.7528 Evaluate side-chains 193 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 406 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 71 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 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 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 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 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 162 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3717 r_free = 0.3717 target = 0.138661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096060 restraints weight = 19453.835| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.57 r_work: 0.2957 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17169 Z= 0.261 Angle : 0.660 8.379 23387 Z= 0.338 Chirality : 0.048 0.188 2609 Planarity : 0.005 0.042 2975 Dihedral : 6.479 58.819 2725 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.07 % Favored : 96.64 % Rotamer: Outliers : 4.75 % Allowed : 19.13 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2117 helix: 2.02 (0.28), residues: 354 sheet: 1.09 (0.21), residues: 603 loop : -1.00 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 36 HIS 0.008 0.001 HIS A 25 PHE 0.028 0.003 PHE A 128 TYR 0.018 0.002 TYR H 95 ARG 0.003 0.000 ARG D 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 12) link_NAG-ASN : angle 1.88972 ( 36) link_BETA1-4 : bond 0.00587 ( 6) link_BETA1-4 : angle 1.78995 ( 18) hydrogen bonds : bond 0.08364 ( 620) hydrogen bonds : angle 4.57135 ( 1746) SS BOND : bond 0.00391 ( 21) SS BOND : angle 1.21504 ( 42) covalent geometry : bond 0.00662 (17130) covalent geometry : angle 0.65285 (23291) *********************** 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 211 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 130 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: A 406 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.5739 (mt0) REVERT: A 494 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6917 (tp30) REVERT: B 30 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7758 (ptm-80) REVERT: D 172 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 188 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7909 (pttt) REVERT: D 222 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: D 373 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: D 374 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6423 (mt0) REVERT: D 494 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6955 (tp30) REVERT: G 129 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: G 172 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: G 310 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.7673 (pp30) REVERT: G 373 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: G 374 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6847 (mt0) REVERT: H 5 VAL cc_start: 0.7952 (t) cc_final: 0.7678 (m) REVERT: F 62 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6272 (ptm-80) outliers start: 81 outliers final: 46 residues processed: 199 average time/residue: 1.4082 time to fit residues: 309.8278 Evaluate side-chains 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 406 GLN Chi-restraints excluded: chain A residue 442 LEU 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 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 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 310 GLN 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 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 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 22 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 115 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN D 173 ASN D 290 HIS D 469 GLN D 486 HIS G 173 ASN G 290 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.143290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101468 restraints weight = 19273.475| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.45 r_work: 0.3039 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17169 Z= 0.106 Angle : 0.488 7.784 23387 Z= 0.255 Chirality : 0.042 0.157 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.844 58.108 2725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.03 % Favored : 97.78 % Rotamer: Outliers : 3.64 % Allowed : 20.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2117 helix: 2.32 (0.28), residues: 357 sheet: 1.30 (0.22), residues: 579 loop : -0.76 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.000 HIS D 370 PHE 0.010 0.001 PHE G 128 TYR 0.009 0.001 TYR G 368 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 12) link_NAG-ASN : angle 1.38841 ( 36) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.38443 ( 18) hydrogen bonds : bond 0.06308 ( 620) hydrogen bonds : angle 4.25606 ( 1746) SS BOND : bond 0.00217 ( 21) SS BOND : angle 1.07275 ( 42) covalent geometry : bond 0.00213 (17130) covalent geometry : angle 0.48224 (23291) *********************** 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 206 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 183 THR cc_start: 0.8157 (t) cc_final: 0.7669 (m) REVERT: A 374 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: A 406 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5830 (mt0) REVERT: A 494 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6946 (tp30) REVERT: B 30 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7635 (ptm-80) REVERT: B 48 MET cc_start: 0.8827 (mtp) cc_final: 0.8451 (mtp) REVERT: D 172 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: D 188 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7845 (pttt) REVERT: D 222 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7514 (ttm170) REVERT: D 373 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: D 374 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6194 (mt0) REVERT: D 494 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6984 (tp30) REVERT: G 129 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: G 172 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: G 188 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7606 (pttt) REVERT: G 373 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: G 374 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6800 (mt0) REVERT: H 5 VAL cc_start: 0.7832 (t) cc_final: 0.7567 (m) REVERT: F 62 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6235 (ptm-80) outliers start: 61 outliers final: 34 residues processed: 194 average time/residue: 1.3477 time to fit residues: 290.7759 Evaluate side-chains 188 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 12 LYS 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 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 366 TYR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 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 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP 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 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 158 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 290 HIS F 52 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.143920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102273 restraints weight = 19271.137| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.44 r_work: 0.3052 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1126 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= 0.100 Angle : 0.477 7.560 23387 Z= 0.247 Chirality : 0.042 0.150 2609 Planarity : 0.004 0.035 2975 Dihedral : 5.550 59.942 2723 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 3.36 % Allowed : 20.97 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2117 helix: 2.56 (0.28), residues: 357 sheet: 1.26 (0.20), residues: 642 loop : -0.79 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 92 HIS 0.003 0.000 HIS A 25 PHE 0.014 0.001 PHE A 128 TYR 0.012 0.001 TYR E 95 ARG 0.002 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 12) link_NAG-ASN : angle 1.32370 ( 36) link_BETA1-4 : bond 0.00535 ( 6) link_BETA1-4 : angle 1.36383 ( 18) hydrogen bonds : bond 0.06015 ( 620) hydrogen bonds : angle 4.10533 ( 1746) SS BOND : bond 0.00229 ( 21) SS BOND : angle 0.97204 ( 42) covalent geometry : bond 0.00206 (17130) covalent geometry : angle 0.47195 (23291) *********************** 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 202 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: A 183 THR cc_start: 0.8109 (t) cc_final: 0.7748 (m) REVERT: A 374 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: A 406 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5921 (mt0) REVERT: A 494 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6965 (tp30) REVERT: D 172 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: D 188 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (pttt) REVERT: D 222 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7556 (ttm170) REVERT: D 374 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6117 (mt0) REVERT: D 494 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7013 (tp30) REVERT: G 129 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: G 172 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: G 188 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7646 (pttt) REVERT: G 374 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: H 5 VAL cc_start: 0.7865 (t) cc_final: 0.7603 (m) REVERT: F 32 ASP cc_start: 0.5955 (OUTLIER) cc_final: 0.5599 (m-30) REVERT: F 62 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6300 (ptm-80) REVERT: F 66 SER cc_start: 0.7227 (t) cc_final: 0.6721 (p) outliers start: 56 outliers final: 32 residues processed: 191 average time/residue: 1.4053 time to fit residues: 296.8368 Evaluate side-chains 186 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 406 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 116 THR 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 331 MET Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain 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 C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 173 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098974 restraints weight = 19440.884| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.49 r_work: 0.3001 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 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 = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1157 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= 0.170 Angle : 0.557 7.651 23387 Z= 0.287 Chirality : 0.045 0.168 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.671 59.486 2717 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 20.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2117 helix: 2.36 (0.28), residues: 357 sheet: 1.17 (0.21), residues: 597 loop : -0.78 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 25 PHE 0.021 0.002 PHE A 128 TYR 0.015 0.001 TYR E 95 ARG 0.002 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 12) link_NAG-ASN : angle 1.59258 ( 36) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 1.50115 ( 18) hydrogen bonds : bond 0.07160 ( 620) hydrogen bonds : angle 4.28759 ( 1746) SS BOND : bond 0.00302 ( 21) SS BOND : angle 1.09423 ( 42) covalent geometry : bond 0.00416 (17130) covalent geometry : angle 0.55086 (23291) *********************** 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 197 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: A 406 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5887 (mt0) REVERT: A 494 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6996 (tp30) REVERT: D 172 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: D 188 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7856 (pttt) REVERT: D 222 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: D 374 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6256 (mt0) REVERT: D 494 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6958 (tp30) REVERT: E 93 MET cc_start: 0.7630 (tpt) cc_final: 0.7417 (tpt) REVERT: G 129 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: G 172 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: G 188 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7684 (pttt) REVERT: G 374 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: H 5 VAL cc_start: 0.7898 (t) cc_final: 0.7633 (m) REVERT: F 62 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6133 (ptm160) REVERT: F 66 SER cc_start: 0.7332 (t) cc_final: 0.6851 (p) outliers start: 55 outliers final: 35 residues processed: 187 average time/residue: 1.3799 time to fit residues: 285.9356 Evaluate side-chains 184 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 406 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 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 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 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 97 THR 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 10 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 130 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094155 restraints weight = 19372.091| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.49 r_work: 0.3033 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 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 = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17169 Z= 0.136 Angle : 0.523 7.549 23387 Z= 0.270 Chirality : 0.044 0.165 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.566 58.319 2717 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 2.96 % Allowed : 21.36 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2117 helix: 2.37 (0.28), residues: 357 sheet: 1.16 (0.21), residues: 612 loop : -0.78 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 92 HIS 0.004 0.001 HIS A 25 PHE 0.018 0.002 PHE D 128 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 12) link_NAG-ASN : angle 1.50746 ( 36) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 1.45320 ( 18) hydrogen bonds : bond 0.06824 ( 620) hydrogen bonds : angle 4.23225 ( 1746) SS BOND : bond 0.00265 ( 21) SS BOND : angle 1.07967 ( 42) covalent geometry : bond 0.00322 (17130) covalent geometry : angle 0.51712 (23291) ********************** 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 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 406 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5822 (mt0) REVERT: A 494 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6903 (tp30) REVERT: D 172 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: D 188 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7785 (pttt) REVERT: D 222 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7527 (ttm170) REVERT: D 374 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6194 (mt0) REVERT: D 494 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6858 (tp30) REVERT: E 93 MET cc_start: 0.7478 (tpt) cc_final: 0.7274 (tpt) REVERT: G 129 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: G 172 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: G 188 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7606 (pttt) REVERT: G 373 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: H 5 VAL cc_start: 0.7807 (t) cc_final: 0.7542 (m) REVERT: F 62 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6071 (ptm160) REVERT: F 66 SER cc_start: 0.7314 (t) cc_final: 0.6834 (p) outliers start: 49 outliers final: 35 residues processed: 181 average time/residue: 1.3985 time to fit residues: 280.4606 Evaluate side-chains 185 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 406 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 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 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 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 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 184 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 175 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095266 restraints weight = 19284.410| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.44 r_work: 0.3048 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1175 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= 0.116 Angle : 0.501 7.444 23387 Z= 0.260 Chirality : 0.043 0.160 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.466 57.918 2717 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.26 % Rotamer: Outliers : 3.02 % Allowed : 21.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2117 helix: 2.44 (0.28), residues: 357 sheet: 1.19 (0.21), residues: 612 loop : -0.74 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 92 HIS 0.003 0.001 HIS A 25 PHE 0.016 0.001 PHE G 128 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.44437 ( 36) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.41579 ( 18) hydrogen bonds : bond 0.06517 ( 620) hydrogen bonds : angle 4.18467 ( 1746) SS BOND : bond 0.00250 ( 21) SS BOND : angle 1.03708 ( 42) covalent geometry : bond 0.00258 (17130) covalent geometry : angle 0.49519 (23291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15188.31 seconds wall clock time: 262 minutes 7.40 seconds (15727.40 seconds total)