Starting phenix.real_space_refine on Wed Jun 25 18:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dim_27440/06_2025/8dim_27440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dim_27440/06_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_27440/06_2025/8dim_27440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dim_27440/06_2025/8dim_27440.map" model { file = "/net/cci-nas-00/data/ceres_data/8dim_27440/06_2025/8dim_27440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dim_27440/06_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-5710/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: 9.96, per 1000 atoms: 0.59 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: 3.81 Conformation dependent library (CDL) restraints added in 2.2 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: 2.32 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: 5.63 Time building geometry restraints manager: 4.57 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: 8.350 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.760 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.110 ------------------------------------------------------------------------------- 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 : 1.716 Fit side-chains outliers start: 59 outliers final: 55 residues processed: 212 average time/residue: 1.1449 time to fit residues: 273.2917 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 : 1.741 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.098309 restraints weight = 19148.615| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.46 r_work: 0.2997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 60.598 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 1.46079 ( 36) link_BETA1-4 : bond 0.00421 ( 6) link_BETA1-4 : angle 2.25372 ( 18) hydrogen bonds : bond 0.07585 ( 620) hydrogen bonds : angle 4.69380 ( 1746) SS BOND : bond 0.00305 ( 21) SS BOND : angle 1.34543 ( 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 : 1.958 Fit side-chains REVERT: A 374 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: A 494 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7003 (tp30) REVERT: B 30 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8330 (mtm-85) REVERT: D 188 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7703 (pttt) REVERT: D 222 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: D 494 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7038 (tp30) REVERT: G 129 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: F 32 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5450 (m-30) REVERT: F 66 SER cc_start: 0.6937 (t) cc_final: 0.6442 (p) outliers start: 76 outliers final: 44 residues processed: 213 average time/residue: 1.2766 time to fit residues: 303.5517 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 : 1.716 ------------------------------------------------------------------------------- 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: 0.0170 chunk 182 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.142605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100533 restraints weight = 19157.952| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.43 r_work: 0.3028 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0736 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= 0.124 Angle : 0.522 9.580 23387 Z= 0.269 Chirality : 0.044 0.158 2609 Planarity : 0.004 0.037 2975 Dihedral : 6.818 59.729 2733 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.03 % Favored : 97.68 % Rotamer: Outliers : 3.97 % Allowed : 19.97 % 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: 0.55 (0.18), residues: 2117 helix: 2.24 (0.28), residues: 357 sheet: 1.27 (0.21), residues: 579 loop : -0.73 (0.17), residues: 1181 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 0.015 0.001 PHE D 128 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.31331 ( 36) link_BETA1-4 : bond 0.00572 ( 6) link_BETA1-4 : angle 1.74194 ( 18) hydrogen bonds : bond 0.06716 ( 620) hydrogen bonds : angle 4.36894 ( 1746) SS BOND : bond 0.00249 ( 21) SS BOND : angle 1.15869 ( 42) covalent geometry : bond 0.00280 (17130) covalent geometry : angle 0.51599 (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 215 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 148 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: A 494 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6921 (tp30) REVERT: B 30 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7440 (ptm-80) REVERT: D 172 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 188 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7754 (pttt) REVERT: D 222 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: D 494 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6985 (tp30) REVERT: G 129 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: G 172 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: G 188 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7538 (pttt) REVERT: G 373 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: G 374 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: F 62 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6293 (ptm-80) outliers start: 67 outliers final: 38 residues processed: 202 average time/residue: 1.3212 time to fit residues: 296.7256 Evaluate side-chains 175 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 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 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 66 SER 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: 1.9990 chunk 26 optimal weight: 0.0970 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.141924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099863 restraints weight = 19242.380| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.45 r_work: 0.3019 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0843 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= 0.137 Angle : 0.536 8.615 23387 Z= 0.276 Chirality : 0.044 0.161 2609 Planarity : 0.004 0.037 2975 Dihedral : 6.290 59.684 2728 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.12 % Rotamer: Outliers : 4.75 % Allowed : 19.02 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.28), residues: 357 sheet: 1.19 (0.21), residues: 597 loop : -0.72 (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 B 95 ARG 0.004 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 12) link_NAG-ASN : angle 1.40913 ( 36) link_BETA1-4 : bond 0.00513 ( 6) link_BETA1-4 : angle 1.64634 ( 18) hydrogen bonds : bond 0.06846 ( 620) hydrogen bonds : angle 4.31332 ( 1746) SS BOND : bond 0.00255 ( 21) SS BOND : angle 1.07786 ( 42) covalent geometry : bond 0.00321 (17130) covalent geometry : angle 0.52986 (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: 81 poor density : 132 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: A 494 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6936 (tp30) REVERT: B 30 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6860 (ptm-80) REVERT: B 106 GLU cc_start: 0.8645 (pm20) cc_final: 0.8439 (pm20) REVERT: D 172 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: D 188 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7790 (pttt) REVERT: D 222 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7555 (ttm170) REVERT: D 373 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: D 374 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6019 (mt0) REVERT: D 494 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6999 (tp30) REVERT: E 93 MET cc_start: 0.7568 (tpt) cc_final: 0.7354 (tpt) REVERT: G 129 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: G 172 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: G 188 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7588 (pttt) REVERT: G 374 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: F 32 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5505 (m-30) REVERT: F 62 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5941 (ptm160) outliers start: 81 outliers final: 44 residues processed: 197 average time/residue: 1.3459 time to fit residues: 295.3150 Evaluate side-chains 187 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 31 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 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 180 ILE 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 366 TYR 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: 5.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.140239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097668 restraints weight = 19528.612| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.57 r_work: 0.2980 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17169 Z= 0.182 Angle : 0.587 8.292 23387 Z= 0.302 Chirality : 0.045 0.177 2609 Planarity : 0.004 0.041 2975 Dihedral : 6.310 58.840 2725 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.51 % Favored : 97.21 % Rotamer: Outliers : 4.64 % Allowed : 19.18 % Favored : 76.17 % 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: 0.39 (0.18), residues: 2117 helix: 2.12 (0.28), residues: 357 sheet: 1.13 (0.21), residues: 603 loop : -0.86 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.006 0.001 HIS A 25 PHE 0.022 0.002 PHE A 128 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 12) link_NAG-ASN : angle 1.66000 ( 36) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 1.62191 ( 18) hydrogen bonds : bond 0.07616 ( 620) hydrogen bonds : angle 4.44889 ( 1746) SS BOND : bond 0.00316 ( 21) SS BOND : angle 1.16547 ( 42) covalent geometry : bond 0.00448 (17130) covalent geometry : angle 0.58069 (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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 133 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: A 406 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.5789 (mt0) REVERT: A 494 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6951 (tp30) REVERT: B 30 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7769 (ptm-80) REVERT: D 172 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: D 188 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7878 (pttt) REVERT: D 222 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7592 (ttm170) REVERT: D 373 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: D 374 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6322 (mt0) REVERT: D 494 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7017 (tp30) REVERT: G 129 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: G 172 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: G 188 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7709 (pttt) REVERT: G 310 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: G 355 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: G 373 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: G 374 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6675 (mt0) REVERT: H 5 VAL cc_start: 0.7924 (t) cc_final: 0.7654 (m) REVERT: F 62 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6255 (ptm-80) outliers start: 79 outliers final: 45 residues processed: 200 average time/residue: 1.4122 time to fit residues: 312.5914 Evaluate side-chains 187 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 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 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 355 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 162 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 D 486 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099268 restraints weight = 19392.460| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.55 r_work: 0.3007 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1008 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= 0.133 Angle : 0.530 8.120 23387 Z= 0.274 Chirality : 0.044 0.167 2609 Planarity : 0.004 0.038 2975 Dihedral : 6.040 57.076 2725 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.36 % Favored : 97.35 % Rotamer: Outliers : 4.53 % Allowed : 19.52 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.18), residues: 2117 helix: 2.24 (0.28), residues: 357 sheet: 1.20 (0.21), residues: 597 loop : -0.80 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.004 0.001 HIS A 25 PHE 0.016 0.002 PHE A 128 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 12) link_NAG-ASN : angle 1.51039 ( 36) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 1.50612 ( 18) hydrogen bonds : bond 0.06951 ( 620) hydrogen bonds : angle 4.32052 ( 1746) SS BOND : bond 0.00259 ( 21) SS BOND : angle 1.10466 ( 42) covalent geometry : bond 0.00307 (17130) covalent geometry : angle 0.52392 (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 213 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: A 406 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5785 (mt0) REVERT: A 494 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6945 (tp30) REVERT: B 30 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7714 (ptm-80) REVERT: D 172 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: D 188 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7891 (pttt) REVERT: D 222 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7568 (ttm170) REVERT: D 373 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: D 374 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6296 (mt0) REVERT: D 494 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7013 (tp30) REVERT: G 129 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: G 172 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: G 188 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7685 (pttt) REVERT: G 374 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6623 (mt0) REVERT: H 5 VAL cc_start: 0.7899 (t) cc_final: 0.7640 (m) REVERT: F 62 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6326 (ptm-80) outliers start: 77 outliers final: 45 residues processed: 199 average time/residue: 1.3704 time to fit residues: 302.2689 Evaluate side-chains 189 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 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 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 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 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 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: 4.9990 chunk 134 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 404 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101271 restraints weight = 19290.677| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.47 r_work: 0.3042 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17169 Z= 0.109 Angle : 0.492 7.807 23387 Z= 0.255 Chirality : 0.043 0.156 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.730 58.304 2725 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.41 % Favored : 97.40 % Rotamer: Outliers : 4.08 % Allowed : 20.02 % 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: 0.59 (0.18), residues: 2117 helix: 2.44 (0.28), residues: 357 sheet: 1.18 (0.21), residues: 597 loop : -0.73 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.003 0.001 HIS G 25 PHE 0.014 0.001 PHE G 128 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 12) link_NAG-ASN : angle 1.37389 ( 36) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.40125 ( 18) hydrogen bonds : bond 0.06329 ( 620) hydrogen bonds : angle 4.17483 ( 1746) SS BOND : bond 0.00238 ( 21) SS BOND : angle 1.02147 ( 42) covalent geometry : bond 0.00235 (17130) covalent geometry : angle 0.48619 (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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 143 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: A 406 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.5907 (mt0) REVERT: A 494 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6965 (tp30) REVERT: B 30 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7660 (ptm-80) REVERT: D 172 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 188 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7836 (pttt) REVERT: D 222 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: D 374 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6169 (mt0) REVERT: D 494 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7027 (tp30) REVERT: E 93 MET cc_start: 0.7510 (tpt) cc_final: 0.7302 (tpt) REVERT: G 129 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: G 172 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: G 188 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7624 (pttt) REVERT: G 355 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8175 (mm-30) REVERT: G 373 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: G 374 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: H 5 VAL cc_start: 0.7882 (t) cc_final: 0.7622 (m) REVERT: F 62 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6375 (ptm-80) outliers start: 69 outliers final: 41 residues processed: 200 average time/residue: 1.3836 time to fit residues: 307.7580 Evaluate side-chains 192 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 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 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.142103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094737 restraints weight = 19267.321| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.49 r_work: 0.3036 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1097 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= 0.129 Angle : 0.515 7.561 23387 Z= 0.266 Chirality : 0.043 0.160 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.654 59.049 2722 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 3.86 % Allowed : 20.41 % 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: 0.57 (0.18), residues: 2117 helix: 2.42 (0.28), residues: 357 sheet: 1.16 (0.21), residues: 597 loop : -0.74 (0.17), residues: 1163 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 0.018 0.002 PHE A 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 0.00146 ( 12) link_NAG-ASN : angle 1.46181 ( 36) link_BETA1-4 : bond 0.00538 ( 6) link_BETA1-4 : angle 1.44423 ( 18) hydrogen bonds : bond 0.06622 ( 620) hydrogen bonds : angle 4.20657 ( 1746) SS BOND : bond 0.00265 ( 21) SS BOND : angle 1.04841 ( 42) covalent geometry : bond 0.00298 (17130) covalent geometry : angle 0.50922 (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 206 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: A 406 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.5814 (mt0) REVERT: A 494 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6895 (tp30) REVERT: B 30 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7588 (ptm-80) REVERT: D 172 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: D 188 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: D 222 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7527 (ttm170) REVERT: D 374 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6090 (mt0) REVERT: D 494 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6928 (tp30) REVERT: G 129 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: G 172 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: G 188 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7538 (pttt) REVERT: G 310 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: G 374 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6511 (mt0) REVERT: H 5 VAL cc_start: 0.7814 (t) cc_final: 0.7541 (m) REVERT: F 62 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6337 (ptm-80) outliers start: 65 outliers final: 44 residues processed: 193 average time/residue: 1.3528 time to fit residues: 289.1616 Evaluate side-chains 197 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 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 147 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 163 optimal weight: 0.0270 chunk 105 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.143042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101161 restraints weight = 19431.433| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.51 r_work: 0.3037 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.1123 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= 0.113 Angle : 0.491 7.393 23387 Z= 0.255 Chirality : 0.043 0.154 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.506 59.941 2722 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.36 % Favored : 97.49 % Rotamer: Outliers : 3.86 % Allowed : 20.13 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.18), residues: 2117 helix: 2.51 (0.28), residues: 357 sheet: 1.22 (0.20), residues: 642 loop : -0.80 (0.18), residues: 1118 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 0.015 0.001 PHE A 128 TYR 0.012 0.001 TYR E 95 ARG 0.002 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 12) link_NAG-ASN : angle 1.38591 ( 36) link_BETA1-4 : bond 0.00543 ( 6) link_BETA1-4 : angle 1.39326 ( 18) hydrogen bonds : bond 0.06321 ( 620) hydrogen bonds : angle 4.15097 ( 1746) SS BOND : bond 0.00252 ( 21) SS BOND : angle 1.02909 ( 42) covalent geometry : bond 0.00252 (17130) covalent geometry : angle 0.48571 (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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 183 THR cc_start: 0.8142 (t) cc_final: 0.7720 (m) REVERT: A 374 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: A 406 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.5869 (mt0) REVERT: A 494 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6990 (tp30) REVERT: B 30 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7605 (ptm-80) REVERT: D 172 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: D 188 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7833 (pttt) REVERT: D 222 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7550 (ttm170) REVERT: D 374 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6101 (mt0) REVERT: D 494 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6991 (tp30) REVERT: E 93 MET cc_start: 0.7437 (tpt) cc_final: 0.7232 (tpp) REVERT: G 129 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: G 172 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: G 188 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7651 (pttt) REVERT: G 310 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: G 373 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: G 374 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6520 (mt0) REVERT: H 5 VAL cc_start: 0.7892 (t) cc_final: 0.7624 (m) REVERT: F 62 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6183 (ptm160) outliers start: 65 outliers final: 44 residues processed: 201 average time/residue: 1.4575 time to fit residues: 325.4234 Evaluate side-chains 203 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 22 ILE 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 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 31 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 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 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 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 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 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: 5.9990 chunk 181 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 68 HIS G 173 ASN G 290 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN 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 = 0.138719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096436 restraints weight = 19448.644| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.50 r_work: 0.2962 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17169 Z= 0.259 Angle : 0.653 7.698 23387 Z= 0.335 Chirality : 0.048 0.187 2609 Planarity : 0.005 0.041 2975 Dihedral : 6.092 59.608 2722 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 3.91 % Allowed : 20.08 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.18), residues: 2117 helix: 2.08 (0.28), residues: 354 sheet: 1.03 (0.21), residues: 603 loop : -0.99 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 36 HIS 0.007 0.001 HIS A 25 PHE 0.028 0.003 PHE A 128 TYR 0.019 0.002 TYR H 95 ARG 0.003 0.000 ARG B 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.88884 ( 36) link_BETA1-4 : bond 0.00553 ( 6) link_BETA1-4 : angle 1.69757 ( 18) hydrogen bonds : bond 0.08264 ( 620) hydrogen bonds : angle 4.52652 ( 1746) SS BOND : bond 0.00399 ( 21) SS BOND : angle 1.22658 ( 42) covalent geometry : bond 0.00660 (17130) covalent geometry : angle 0.64652 (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 199 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 133 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: A 406 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5757 (mt0) REVERT: A 494 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6882 (tp30) REVERT: B 30 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7805 (ptm-80) REVERT: D 172 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: D 188 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7929 (pttt) REVERT: D 374 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6388 (mt0) REVERT: D 494 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6939 (tp30) REVERT: E 93 MET cc_start: 0.7691 (tpt) cc_final: 0.7488 (tpp) REVERT: G 129 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: G 172 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 188 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7764 (pttt) REVERT: G 310 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: G 373 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: G 374 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6715 (mt0) REVERT: H 5 VAL cc_start: 0.7960 (t) cc_final: 0.7684 (m) REVERT: F 62 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6175 (ptm160) outliers start: 66 outliers final: 43 residues processed: 193 average time/residue: 1.4133 time to fit residues: 301.8259 Evaluate side-chains 185 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain 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 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 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 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 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 184 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101028 restraints weight = 19303.662| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.45 r_work: 0.3031 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17169 Z= 0.112 Angle : 0.491 7.187 23387 Z= 0.256 Chirality : 0.043 0.160 2609 Planarity : 0.004 0.038 2975 Dihedral : 5.592 58.127 2722 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.17 % Favored : 97.68 % Rotamer: Outliers : 3.13 % Allowed : 20.86 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2117 helix: 2.37 (0.28), residues: 357 sheet: 1.13 (0.21), residues: 612 loop : -0.81 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 92 HIS 0.003 0.001 HIS A 25 PHE 0.013 0.001 PHE D 128 TYR 0.010 0.001 TYR E 95 ARG 0.002 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 12) link_NAG-ASN : angle 1.44063 ( 36) link_BETA1-4 : bond 0.00502 ( 6) link_BETA1-4 : angle 1.38404 ( 18) hydrogen bonds : bond 0.06490 ( 620) hydrogen bonds : angle 4.22241 ( 1746) SS BOND : bond 0.00246 ( 21) SS BOND : angle 1.09572 ( 42) covalent geometry : bond 0.00242 (17130) covalent geometry : angle 0.48473 (23291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16443.53 seconds wall clock time: 281 minutes 19.80 seconds (16879.80 seconds total)