Starting phenix.real_space_refine on Sun Jun 15 13:42:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.map" model { file = "/net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txu_41705/06_2025/8txu_41705.cif" } resolution = 3.22 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10909 2.51 5 N 2963 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 17503 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "B" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "C" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "G" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.71, per 1000 atoms: 0.61 Number of scatterers: 17503 At special positions: 0 Unit cell: (145.25, 136.95, 146.91, 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 84 16.00 O 3547 8.00 N 2963 7.00 C 10909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.02 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 402 " - " ASN A 63 " " NAG A 403 " - " ASN A 126 " " NAG A 404 " - " ASN A 133 " " NAG B 301 " - " ASN B 154 " Time building additional restraints: 4.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3978 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 47 sheets defined 16.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.596A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 80' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.186A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 111 Processing helix chain 'B' and resid 115 through 124 removed outlier: 4.174A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.919A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 111 Processing helix chain 'D' and resid 114 through 127 removed outlier: 4.593A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 65 through 71 Processing helix chain 'G' and resid 104 through 116 Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 37 through 54 removed outlier: 4.035A pdb=" N ARG I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 111 removed outlier: 3.614A pdb=" N ASP I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 127 removed outlier: 4.610A pdb=" N LYS I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN I 125 " --> pdb=" O LYS I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.652A pdb=" N ILE I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.635A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.554A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE J 83 " --> pdb=" O GLN J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.963A pdb=" N LYS F 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.735A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.606A pdb=" N ASP K 82 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE K 83 " --> pdb=" O GLN K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.611A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.759A pdb=" N PHE B 138 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.607A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.621A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.658A pdb=" N THR A 155 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 7.145A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.935A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.577A pdb=" N GLY A 303 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 28 removed outlier: 3.532A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN B 28 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.510A pdb=" N THR C 40 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.437A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.741A pdb=" N ARG C 90 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.599A pdb=" N LEU C 154 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 251 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.934A pdb=" N LEU C 243 " --> pdb=" O MET C 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 179 through 184 Processing sheet with id=AC4, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.666A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 52 removed outlier: 6.619A pdb=" N ILE G 51 " --> pdb=" O GLY G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 3.620A pdb=" N VAL G 88 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AD2, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.943A pdb=" N LEU G 243 " --> pdb=" O MET G 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 179 through 184 Processing sheet with id=AD4, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.716A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 81 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.667A pdb=" N GLU E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.818A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AE1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.477A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.637A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.567A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.812A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.758A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.669A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.669A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1407 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: 6.79 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5553 1.34 - 1.46: 4414 1.46 - 1.59: 7776 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 17857 Sorted by residual: bond pdb=" N CYS G 14 " pdb=" CA CYS G 14 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N ASP A 225 " pdb=" CA ASP A 225 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.45e+00 bond pdb=" N ASN G 31 " pdb=" CA ASN G 31 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.79e+00 bond pdb=" N ILE G 29 " pdb=" CA ILE G 29 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.34e-02 5.57e+03 8.77e+00 bond pdb=" N LEU B 126 " pdb=" CA LEU B 126 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.16e-02 7.43e+03 8.27e+00 ... (remaining 17852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23083 2.08 - 4.16: 888 4.16 - 6.25: 169 6.25 - 8.33: 22 8.33 - 10.41: 14 Bond angle restraints: 24176 Sorted by residual: angle pdb=" C TYR J 50 " pdb=" N THR J 51 " pdb=" CA THR J 51 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C SER K 30 " pdb=" CA SER K 30 " pdb=" CB SER K 30 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C TYR L 50 " pdb=" N THR L 51 " pdb=" CA THR L 51 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C TYR K 50 " pdb=" N THR K 51 " pdb=" CA THR K 51 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C THR G 12 " pdb=" CA THR G 12 " pdb=" CB THR G 12 " ideal model delta sigma weight residual 111.78 102.22 9.56 1.98e+00 2.55e-01 2.33e+01 ... (remaining 24171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 10331 22.09 - 44.18: 733 44.18 - 66.28: 83 66.28 - 88.37: 73 88.37 - 110.46: 48 Dihedral angle restraints: 11268 sinusoidal: 5040 harmonic: 6228 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 156.45 -63.45 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -22.66 -63.34 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.21 -62.21 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2341 0.074 - 0.148: 366 0.148 - 0.222: 35 0.222 - 0.296: 13 0.296 - 0.370: 2 Chirality restraints: 2757 Sorted by residual: chirality pdb=" CB VAL D 77 " pdb=" CA VAL D 77 " pdb=" CG1 VAL D 77 " pdb=" CG2 VAL D 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU A 71 " pdb=" CB LEU A 71 " pdb=" CD1 LEU A 71 " pdb=" CD2 LEU A 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CG LEU A 13 " pdb=" CB LEU A 13 " pdb=" CD1 LEU A 13 " pdb=" CD2 LEU A 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2754 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 13 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO E 14 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 126 " 0.008 2.00e-02 2.50e+03 3.93e-02 1.93e+01 pdb=" CG ASN A 126 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 126 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 126 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 20 " -0.065 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO C 21 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " -0.053 5.00e-02 4.00e+02 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 25 2.37 - 3.00: 8891 3.00 - 3.63: 25534 3.63 - 4.27: 39872 4.27 - 4.90: 66756 Nonbonded interactions: 141078 Sorted by model distance: nonbonded pdb=" ND2 ASN G 8 " pdb=" OG1 THR G 12 " model vdw 1.731 3.120 nonbonded pdb=" ND2 ASN G 8 " pdb=" CB THR G 12 " model vdw 2.014 3.550 nonbonded pdb=" ND2 ASN G 8 " pdb=" CG2 THR G 12 " model vdw 2.055 3.540 nonbonded pdb=" O GLN H 62 " pdb=" NZ LYS H 65 " model vdw 2.259 3.120 nonbonded pdb=" O THR L 8 " pdb=" OG1 THR L 102 " model vdw 2.272 3.040 ... (remaining 141073 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 1 through 325) selection = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 1 through 168) selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.560 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 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 : 0.005 0.048 17912 Z= 0.263 Angle : 0.946 10.411 24320 Z= 0.491 Chirality : 0.056 0.370 2757 Planarity : 0.006 0.113 3065 Dihedral : 17.719 110.461 7227 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 0.37 % Allowed : 0.75 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.05 (0.18), residues: 2139 helix: -0.17 (0.27), residues: 297 sheet: -0.92 (0.22), residues: 609 loop : -1.95 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 14 HIS 0.013 0.002 HIS G 18 PHE 0.034 0.002 PHE I 9 TYR 0.027 0.002 TYR B 141 ARG 0.010 0.001 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 4) link_NAG-ASN : angle 4.00993 ( 12) link_ALPHA1-6 : bond 0.00404 ( 6) link_ALPHA1-6 : angle 1.47651 ( 18) link_BETA1-4 : bond 0.00611 ( 18) link_BETA1-4 : angle 1.50383 ( 54) link_ALPHA1-3 : bond 0.00364 ( 6) link_ALPHA1-3 : angle 1.52798 ( 18) hydrogen bonds : bond 0.21509 ( 516) hydrogen bonds : angle 8.79583 ( 1407) SS BOND : bond 0.00420 ( 21) SS BOND : angle 1.79383 ( 42) covalent geometry : bond 0.00511 (17857) covalent geometry : angle 0.93695 (24176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 600 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6191 (t0) cc_final: 0.5981 (t0) REVERT: A 169 PRO cc_start: 0.7381 (Cg_endo) cc_final: 0.7059 (Cg_exo) REVERT: A 173 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 262 SER cc_start: 0.8640 (m) cc_final: 0.8358 (p) REVERT: B 22 TYR cc_start: 0.7106 (m-10) cc_final: 0.6847 (m-80) REVERT: B 67 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6729 (tt0) REVERT: C 79 PHE cc_start: 0.7184 (m-10) cc_final: 0.6502 (m-10) REVERT: C 276 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7194 (mmmt) REVERT: D 67 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6787 (tt0) REVERT: D 69 GLU cc_start: 0.7630 (tt0) cc_final: 0.6962 (pt0) REVERT: D 128 GLU cc_start: 0.5692 (tm-30) cc_final: 0.4751 (tt0) REVERT: D 133 MET cc_start: 0.3306 (tmm) cc_final: 0.2623 (tpt) REVERT: G 188 ASP cc_start: 0.6199 (t0) cc_final: 0.5804 (p0) REVERT: G 262 SER cc_start: 0.8589 (t) cc_final: 0.8378 (p) REVERT: G 276 LYS cc_start: 0.7386 (mmtm) cc_final: 0.7152 (mmmt) REVERT: I 67 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6835 (tt0) REVERT: I 69 GLU cc_start: 0.7197 (tt0) cc_final: 0.6959 (pt0) REVERT: I 93 SER cc_start: 0.8734 (p) cc_final: 0.8529 (t) REVERT: E 43 GLN cc_start: 0.6334 (mt0) cc_final: 0.5891 (mt0) REVERT: E 103 SER cc_start: 0.6794 (m) cc_final: 0.6575 (p) REVERT: J 3 GLN cc_start: 0.6539 (pp30) cc_final: 0.5985 (mp10) REVERT: J 51 THR cc_start: 0.6694 (t) cc_final: 0.6128 (t) REVERT: J 74 THR cc_start: 0.7637 (m) cc_final: 0.7432 (m) REVERT: K 18 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7123 (ttm170) REVERT: H 28 THR cc_start: 0.7499 (m) cc_final: 0.6891 (p) REVERT: H 32 TYR cc_start: 0.7672 (m-80) cc_final: 0.7430 (m-80) REVERT: H 103 SER cc_start: 0.7101 (m) cc_final: 0.6783 (p) REVERT: L 29 ILE cc_start: 0.6861 (pt) cc_final: 0.6438 (pt) outliers start: 7 outliers final: 0 residues processed: 603 average time/residue: 0.3167 time to fit residues: 285.1824 Evaluate side-chains 364 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 296 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 129 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN G 158 ASN G 191 GLN G 250 ASN I 42 GLN ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 77 ASN J 89 GLN F 5 GLN K 77 ASN L 3 GLN L 77 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.151332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.136210 restraints weight = 41379.455| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.85 r_work: 0.4093 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17912 Z= 0.159 Angle : 0.697 8.285 24320 Z= 0.362 Chirality : 0.046 0.272 2757 Planarity : 0.005 0.076 3065 Dihedral : 14.082 92.330 3228 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.88 % Allowed : 13.53 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.79 (0.18), residues: 2139 helix: 0.33 (0.28), residues: 321 sheet: -0.94 (0.21), residues: 636 loop : -1.78 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 36 HIS 0.008 0.001 HIS G 18 PHE 0.016 0.001 PHE C 148 TYR 0.032 0.002 TYR H 101 ARG 0.006 0.001 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 4) link_NAG-ASN : angle 2.27822 ( 12) link_ALPHA1-6 : bond 0.00663 ( 6) link_ALPHA1-6 : angle 1.82226 ( 18) link_BETA1-4 : bond 0.00491 ( 18) link_BETA1-4 : angle 1.87016 ( 54) link_ALPHA1-3 : bond 0.00768 ( 6) link_ALPHA1-3 : angle 2.69523 ( 18) hydrogen bonds : bond 0.05002 ( 516) hydrogen bonds : angle 6.45997 ( 1407) SS BOND : bond 0.00542 ( 21) SS BOND : angle 1.26335 ( 42) covalent geometry : bond 0.00350 (17857) covalent geometry : angle 0.68371 (24176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 396 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6383 (t0) cc_final: 0.6081 (t0) REVERT: A 127 TRP cc_start: 0.8194 (m-10) cc_final: 0.7914 (m-10) REVERT: A 191 GLN cc_start: 0.5566 (tt0) cc_final: 0.5076 (tt0) REVERT: A 262 SER cc_start: 0.8762 (m) cc_final: 0.8466 (p) REVERT: B 67 GLU cc_start: 0.7946 (mm-30) cc_final: 0.6693 (tt0) REVERT: B 128 GLU cc_start: 0.4936 (tt0) cc_final: 0.3629 (tp30) REVERT: B 133 MET cc_start: 0.4493 (tpt) cc_final: 0.4188 (tpt) REVERT: C 79 PHE cc_start: 0.7481 (m-10) cc_final: 0.6590 (m-10) REVERT: C 172 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6327 (mp0) REVERT: C 276 LYS cc_start: 0.7587 (mmtm) cc_final: 0.7244 (mmmt) REVERT: D 69 GLU cc_start: 0.7835 (tt0) cc_final: 0.7375 (pt0) REVERT: D 123 LYS cc_start: 0.7764 (tptt) cc_final: 0.7361 (pptt) REVERT: D 128 GLU cc_start: 0.5918 (tm-30) cc_final: 0.4910 (tt0) REVERT: D 129 ASN cc_start: 0.3214 (OUTLIER) cc_final: 0.3012 (p0) REVERT: D 133 MET cc_start: 0.3638 (tmm) cc_final: 0.2841 (tpt) REVERT: G 188 ASP cc_start: 0.6295 (t0) cc_final: 0.5821 (p0) REVERT: G 276 LYS cc_start: 0.7473 (mmtm) cc_final: 0.7240 (mmmt) REVERT: I 67 GLU cc_start: 0.7860 (mm-30) cc_final: 0.6799 (tt0) REVERT: I 69 GLU cc_start: 0.7514 (tt0) cc_final: 0.6911 (pt0) REVERT: I 90 ASP cc_start: 0.8379 (m-30) cc_final: 0.7977 (m-30) REVERT: E 43 GLN cc_start: 0.5486 (mt0) cc_final: 0.4873 (mt0) REVERT: E 55 ASP cc_start: 0.7486 (t0) cc_final: 0.7229 (t0) REVERT: E 103 SER cc_start: 0.7234 (m) cc_final: 0.6951 (p) REVERT: J 3 GLN cc_start: 0.6193 (pp30) cc_final: 0.5526 (mp10) REVERT: J 4 MET cc_start: 0.7084 (ttm) cc_final: 0.6812 (ttm) REVERT: J 92 ASN cc_start: 0.8133 (t0) cc_final: 0.7880 (m-40) REVERT: F 55 ASP cc_start: 0.7819 (t0) cc_final: 0.7570 (t0) REVERT: F 69 ARG cc_start: 0.6919 (ptp-170) cc_final: 0.6227 (ptp-170) REVERT: F 80 TYR cc_start: 0.5620 (m-80) cc_final: 0.5299 (m-80) REVERT: K 18 ARG cc_start: 0.7655 (ttt90) cc_final: 0.7224 (ttm170) REVERT: H 28 THR cc_start: 0.7496 (m) cc_final: 0.6826 (p) REVERT: H 32 TYR cc_start: 0.8168 (m-80) cc_final: 0.7845 (m-80) REVERT: H 103 SER cc_start: 0.7529 (m) cc_final: 0.7062 (p) REVERT: L 31 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7682 (t0) REVERT: L 34 ASN cc_start: 0.8111 (m-40) cc_final: 0.7368 (m-40) REVERT: L 86 TYR cc_start: 0.6110 (m-80) cc_final: 0.5829 (m-80) outliers start: 54 outliers final: 34 residues processed: 424 average time/residue: 0.2783 time to fit residues: 179.3362 Evaluate side-chains 377 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 191 GLN Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 296 ASN B 12 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.147506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.132013 restraints weight = 41042.891| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.84 r_work: 0.4035 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17912 Z= 0.168 Angle : 0.686 8.911 24320 Z= 0.354 Chirality : 0.046 0.283 2757 Planarity : 0.005 0.062 3065 Dihedral : 11.914 89.486 3228 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.62 % Allowed : 15.28 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.71 (0.18), residues: 2139 helix: 0.51 (0.28), residues: 321 sheet: -0.93 (0.22), residues: 597 loop : -1.74 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 47 HIS 0.008 0.001 HIS G 18 PHE 0.018 0.001 PHE C 148 TYR 0.030 0.002 TYR C 195 ARG 0.006 0.001 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 4) link_NAG-ASN : angle 2.11403 ( 12) link_ALPHA1-6 : bond 0.00819 ( 6) link_ALPHA1-6 : angle 1.87925 ( 18) link_BETA1-4 : bond 0.00501 ( 18) link_BETA1-4 : angle 1.70014 ( 54) link_ALPHA1-3 : bond 0.01199 ( 6) link_ALPHA1-3 : angle 2.19603 ( 18) hydrogen bonds : bond 0.04331 ( 516) hydrogen bonds : angle 5.90591 ( 1407) SS BOND : bond 0.00351 ( 21) SS BOND : angle 1.15947 ( 42) covalent geometry : bond 0.00367 (17857) covalent geometry : angle 0.67531 (24176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 366 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6562 (t0) cc_final: 0.6222 (t0) REVERT: A 75 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: A 262 SER cc_start: 0.8783 (m) cc_final: 0.8289 (p) REVERT: B 67 GLU cc_start: 0.7994 (mm-30) cc_final: 0.6657 (tt0) REVERT: B 128 GLU cc_start: 0.5085 (tt0) cc_final: 0.3804 (tp30) REVERT: B 133 MET cc_start: 0.4575 (tpt) cc_final: 0.4205 (tpt) REVERT: C 79 PHE cc_start: 0.7510 (m-10) cc_final: 0.6439 (m-10) REVERT: C 172 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6327 (mp0) REVERT: C 276 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7536 (mmmt) REVERT: C 320 MET cc_start: 0.8573 (ppp) cc_final: 0.8202 (ppp) REVERT: D 32 ARG cc_start: 0.6878 (ptp-170) cc_final: 0.6108 (ptp-170) REVERT: D 37 ASP cc_start: 0.7811 (t0) cc_final: 0.7582 (t70) REVERT: D 69 GLU cc_start: 0.7915 (tt0) cc_final: 0.7418 (pt0) REVERT: D 128 GLU cc_start: 0.6295 (tm-30) cc_final: 0.5216 (tt0) REVERT: D 133 MET cc_start: 0.3989 (tmm) cc_final: 0.3182 (tpt) REVERT: D 167 LEU cc_start: 0.2804 (OUTLIER) cc_final: 0.2510 (mm) REVERT: G 14 CYS cc_start: 0.7673 (m) cc_final: 0.7470 (t) REVERT: G 104 ASP cc_start: 0.8339 (t0) cc_final: 0.8061 (t0) REVERT: G 276 LYS cc_start: 0.7651 (mmtm) cc_final: 0.7359 (mmmt) REVERT: I 67 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6782 (tt0) REVERT: I 69 GLU cc_start: 0.7561 (tt0) cc_final: 0.7023 (pt0) REVERT: I 90 ASP cc_start: 0.8341 (m-30) cc_final: 0.7922 (m-30) REVERT: E 43 GLN cc_start: 0.5512 (mt0) cc_final: 0.4495 (mt0) REVERT: E 55 ASP cc_start: 0.7589 (t0) cc_final: 0.7250 (t0) REVERT: E 81 MET cc_start: 0.4825 (OUTLIER) cc_final: 0.4118 (mtp) REVERT: E 103 SER cc_start: 0.7450 (m) cc_final: 0.7198 (p) REVERT: J 3 GLN cc_start: 0.5885 (pp30) cc_final: 0.5415 (mp10) REVERT: J 4 MET cc_start: 0.6861 (ttm) cc_final: 0.6430 (ttt) REVERT: J 18 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.6968 (ttm170) REVERT: J 92 ASN cc_start: 0.8100 (t0) cc_final: 0.7849 (m-40) REVERT: F 4 LEU cc_start: 0.6692 (mt) cc_final: 0.6461 (mp) REVERT: F 55 ASP cc_start: 0.7916 (t0) cc_final: 0.7635 (t0) REVERT: K 18 ARG cc_start: 0.7529 (ttt90) cc_final: 0.7080 (ttm110) REVERT: H 28 THR cc_start: 0.7433 (m) cc_final: 0.6843 (p) REVERT: H 36 TRP cc_start: 0.7049 (m100) cc_final: 0.6515 (m-10) REVERT: H 55 ASP cc_start: 0.7776 (t0) cc_final: 0.7575 (t0) REVERT: H 103 SER cc_start: 0.7709 (m) cc_final: 0.7238 (p) REVERT: L 31 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7859 (t0) REVERT: L 54 LEU cc_start: 0.6037 (tp) cc_final: 0.5448 (pt) REVERT: L 92 ASN cc_start: 0.7971 (t0) cc_final: 0.7622 (m-40) outliers start: 68 outliers final: 42 residues processed: 405 average time/residue: 0.2639 time to fit residues: 165.1810 Evaluate side-chains 369 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 180 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 156 HIS C 197 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.145371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.129679 restraints weight = 41616.117| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.90 r_work: 0.4000 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17912 Z= 0.164 Angle : 0.672 9.402 24320 Z= 0.345 Chirality : 0.046 0.299 2757 Planarity : 0.004 0.060 3065 Dihedral : 10.531 85.952 3228 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.89 % Allowed : 16.67 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.18), residues: 2139 helix: 0.49 (0.28), residues: 333 sheet: -1.11 (0.21), residues: 615 loop : -1.74 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.008 0.001 HIS G 18 PHE 0.019 0.001 PHE C 148 TYR 0.017 0.002 TYR C 195 ARG 0.004 0.000 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 2.12689 ( 12) link_ALPHA1-6 : bond 0.00900 ( 6) link_ALPHA1-6 : angle 1.98650 ( 18) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 1.59029 ( 54) link_ALPHA1-3 : bond 0.01167 ( 6) link_ALPHA1-3 : angle 2.27235 ( 18) hydrogen bonds : bond 0.04164 ( 516) hydrogen bonds : angle 5.87301 ( 1407) SS BOND : bond 0.00452 ( 21) SS BOND : angle 1.29742 ( 42) covalent geometry : bond 0.00362 (17857) covalent geometry : angle 0.66103 (24176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 340 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6675 (t0) cc_final: 0.6308 (t0) REVERT: A 75 GLN cc_start: 0.8114 (tp40) cc_final: 0.7724 (tt0) REVERT: A 118 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 187 THR cc_start: 0.6910 (p) cc_final: 0.6708 (p) REVERT: A 245 ILE cc_start: 0.8605 (mm) cc_final: 0.8263 (mm) REVERT: A 262 SER cc_start: 0.8807 (m) cc_final: 0.8278 (p) REVERT: B 128 GLU cc_start: 0.4949 (tt0) cc_final: 0.3814 (tp30) REVERT: B 133 MET cc_start: 0.4736 (tpt) cc_final: 0.4411 (tpt) REVERT: C 62 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6728 (mt-10) REVERT: C 79 PHE cc_start: 0.7503 (m-10) cc_final: 0.6525 (m-80) REVERT: C 159 TYR cc_start: 0.6017 (m-10) cc_final: 0.5786 (m-10) REVERT: C 172 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6509 (mp0) REVERT: D 9 PHE cc_start: 0.6970 (p90) cc_final: 0.6715 (p90) REVERT: D 37 ASP cc_start: 0.7839 (t0) cc_final: 0.7550 (t70) REVERT: D 69 GLU cc_start: 0.7884 (tt0) cc_final: 0.7402 (pt0) REVERT: D 128 GLU cc_start: 0.6110 (tm-30) cc_final: 0.5014 (tt0) REVERT: D 133 MET cc_start: 0.4432 (tmm) cc_final: 0.3508 (tpt) REVERT: D 167 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2473 (mm) REVERT: G 311 HIS cc_start: 0.7633 (m90) cc_final: 0.7220 (m90) REVERT: I 37 ASP cc_start: 0.6965 (t70) cc_final: 0.6458 (t70) REVERT: I 67 GLU cc_start: 0.7860 (mm-30) cc_final: 0.6699 (tt0) REVERT: I 69 GLU cc_start: 0.7646 (tt0) cc_final: 0.7119 (pt0) REVERT: I 90 ASP cc_start: 0.8388 (m-30) cc_final: 0.7976 (m-30) REVERT: E 43 GLN cc_start: 0.5392 (mt0) cc_final: 0.5116 (mt0) REVERT: E 55 ASP cc_start: 0.7560 (t0) cc_final: 0.7088 (t0) REVERT: E 94 TYR cc_start: 0.7979 (m-80) cc_final: 0.7646 (m-80) REVERT: E 103 SER cc_start: 0.7445 (m) cc_final: 0.7189 (p) REVERT: J 3 GLN cc_start: 0.5729 (pp30) cc_final: 0.5325 (mp10) REVERT: J 4 MET cc_start: 0.6742 (ttm) cc_final: 0.6411 (ttt) REVERT: J 18 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.6999 (ttm110) REVERT: J 53 ARG cc_start: 0.7074 (mtm180) cc_final: 0.6812 (mtm180) REVERT: J 92 ASN cc_start: 0.8176 (t0) cc_final: 0.7884 (m-40) REVERT: F 4 LEU cc_start: 0.6786 (mt) cc_final: 0.6529 (mp) REVERT: F 80 TYR cc_start: 0.5867 (m-80) cc_final: 0.5493 (m-10) REVERT: K 18 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7027 (ttm110) REVERT: K 29 ILE cc_start: 0.7462 (pt) cc_final: 0.7212 (pt) REVERT: K 30 SER cc_start: 0.7773 (t) cc_final: 0.6847 (m) REVERT: H 28 THR cc_start: 0.7546 (m) cc_final: 0.6946 (p) REVERT: H 36 TRP cc_start: 0.6922 (m100) cc_final: 0.6620 (m-10) REVERT: H 55 ASP cc_start: 0.7944 (t0) cc_final: 0.7720 (t0) REVERT: H 103 SER cc_start: 0.7705 (m) cc_final: 0.7308 (p) REVERT: L 18 ARG cc_start: 0.7620 (ttt-90) cc_final: 0.6988 (ttm170) REVERT: L 24 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7865 (mtp85) REVERT: L 54 LEU cc_start: 0.6084 (tp) cc_final: 0.5659 (pt) outliers start: 73 outliers final: 47 residues processed: 384 average time/residue: 0.2851 time to fit residues: 167.0887 Evaluate side-chains 365 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 0.0050 chunk 127 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 22 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN K 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.119679 restraints weight = 41648.908| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.82 r_work: 0.3867 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 17912 Z= 0.292 Angle : 0.825 11.685 24320 Z= 0.426 Chirality : 0.050 0.322 2757 Planarity : 0.006 0.056 3065 Dihedral : 10.074 84.409 3228 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.44 % Favored : 90.51 % Rotamer: Outliers : 5.17 % Allowed : 17.78 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.24 (0.17), residues: 2139 helix: -0.05 (0.27), residues: 336 sheet: -1.32 (0.21), residues: 588 loop : -2.04 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 47 HIS 0.010 0.002 HIS C 18 PHE 0.022 0.002 PHE C 148 TYR 0.031 0.003 TYR G 98 ARG 0.008 0.001 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 4) link_NAG-ASN : angle 2.73008 ( 12) link_ALPHA1-6 : bond 0.01240 ( 6) link_ALPHA1-6 : angle 1.97755 ( 18) link_BETA1-4 : bond 0.00558 ( 18) link_BETA1-4 : angle 1.61681 ( 54) link_ALPHA1-3 : bond 0.01177 ( 6) link_ALPHA1-3 : angle 2.28678 ( 18) hydrogen bonds : bond 0.05070 ( 516) hydrogen bonds : angle 6.32375 ( 1407) SS BOND : bond 0.00851 ( 21) SS BOND : angle 1.59519 ( 42) covalent geometry : bond 0.00656 (17857) covalent geometry : angle 0.81496 (24176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 325 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7107 (t0) cc_final: 0.6708 (t0) REVERT: A 75 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 230 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7311 (tp) REVERT: B 128 GLU cc_start: 0.5044 (tt0) cc_final: 0.3994 (tp30) REVERT: B 133 MET cc_start: 0.5076 (tpt) cc_final: 0.4603 (tpt) REVERT: C 62 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6515 (mt-10) REVERT: C 79 PHE cc_start: 0.7869 (m-10) cc_final: 0.6982 (m-80) REVERT: C 159 TYR cc_start: 0.6250 (m-10) cc_final: 0.6032 (m-10) REVERT: C 172 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6701 (mp0) REVERT: D 37 ASP cc_start: 0.8252 (t0) cc_final: 0.7903 (t70) REVERT: D 69 GLU cc_start: 0.7971 (tt0) cc_final: 0.7561 (pt0) REVERT: D 128 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5194 (tt0) REVERT: I 17 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5718 (mmp) REVERT: I 69 GLU cc_start: 0.7799 (tt0) cc_final: 0.7408 (pt0) REVERT: I 90 ASP cc_start: 0.8475 (m-30) cc_final: 0.8270 (m-30) REVERT: E 43 GLN cc_start: 0.5875 (mt0) cc_final: 0.5601 (mt0) REVERT: E 55 ASP cc_start: 0.7804 (t0) cc_final: 0.7353 (t0) REVERT: E 103 SER cc_start: 0.7770 (m) cc_final: 0.7483 (p) REVERT: J 3 GLN cc_start: 0.6093 (pp30) cc_final: 0.5366 (mp10) REVERT: J 4 MET cc_start: 0.6883 (ttm) cc_final: 0.6446 (ttt) REVERT: J 18 ARG cc_start: 0.7544 (ttt-90) cc_final: 0.6932 (ttm110) REVERT: J 46 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5950 (mp) REVERT: F 80 TYR cc_start: 0.6205 (m-80) cc_final: 0.5918 (m-80) REVERT: K 18 ARG cc_start: 0.7291 (ttt90) cc_final: 0.6918 (ttm110) REVERT: K 29 ILE cc_start: 0.7741 (pt) cc_final: 0.7521 (pt) REVERT: K 30 SER cc_start: 0.7654 (t) cc_final: 0.6917 (m) REVERT: K 73 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6850 (mp) REVERT: H 36 TRP cc_start: 0.7070 (m100) cc_final: 0.6847 (m-10) REVERT: H 55 ASP cc_start: 0.8127 (t0) cc_final: 0.7896 (t0) REVERT: H 86 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4986 (mp) REVERT: H 103 SER cc_start: 0.7938 (m) cc_final: 0.7576 (p) outliers start: 97 outliers final: 62 residues processed: 383 average time/residue: 0.2684 time to fit residues: 158.2212 Evaluate side-chains 374 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 29 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 75 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN C 296 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.137164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.121033 restraints weight = 41327.997| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.82 r_work: 0.3883 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17912 Z= 0.200 Angle : 0.730 10.476 24320 Z= 0.376 Chirality : 0.047 0.298 2757 Planarity : 0.005 0.053 3065 Dihedral : 9.545 79.132 3228 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.27 % Favored : 91.68 % Rotamer: Outliers : 4.47 % Allowed : 19.97 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.20 (0.17), residues: 2139 helix: -0.01 (0.27), residues: 333 sheet: -1.35 (0.21), residues: 597 loop : -1.98 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 35 HIS 0.009 0.001 HIS G 18 PHE 0.022 0.002 PHE C 148 TYR 0.016 0.002 TYR J 86 ARG 0.007 0.001 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 2.49660 ( 12) link_ALPHA1-6 : bond 0.01141 ( 6) link_ALPHA1-6 : angle 1.98087 ( 18) link_BETA1-4 : bond 0.00435 ( 18) link_BETA1-4 : angle 1.51831 ( 54) link_ALPHA1-3 : bond 0.01028 ( 6) link_ALPHA1-3 : angle 2.20123 ( 18) hydrogen bonds : bond 0.04635 ( 516) hydrogen bonds : angle 6.11860 ( 1407) SS BOND : bond 0.00687 ( 21) SS BOND : angle 2.13481 ( 42) covalent geometry : bond 0.00445 (17857) covalent geometry : angle 0.71679 (24176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 334 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7069 (t0) cc_final: 0.6677 (t0) REVERT: A 75 GLN cc_start: 0.7824 (tp40) cc_final: 0.7483 (tt0) REVERT: A 147 PHE cc_start: 0.5956 (t80) cc_final: 0.5727 (t80) REVERT: A 151 LEU cc_start: 0.8143 (mt) cc_final: 0.7875 (mt) REVERT: B 122 THR cc_start: 0.8496 (m) cc_final: 0.8222 (m) REVERT: B 128 GLU cc_start: 0.4964 (tt0) cc_final: 0.3930 (tp30) REVERT: B 133 MET cc_start: 0.4992 (tpt) cc_final: 0.4572 (tpt) REVERT: C 79 PHE cc_start: 0.7901 (m-10) cc_final: 0.6974 (m-80) REVERT: C 119 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 159 TYR cc_start: 0.6251 (m-10) cc_final: 0.6026 (m-10) REVERT: C 172 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6634 (mp0) REVERT: D 37 ASP cc_start: 0.8269 (t0) cc_final: 0.7915 (t70) REVERT: D 69 GLU cc_start: 0.7899 (tt0) cc_final: 0.7489 (pt0) REVERT: D 128 GLU cc_start: 0.6310 (tm-30) cc_final: 0.5266 (tt0) REVERT: G 17 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7325 (m170) REVERT: I 17 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5220 (mmp) REVERT: I 69 GLU cc_start: 0.7828 (tt0) cc_final: 0.7399 (pt0) REVERT: I 90 ASP cc_start: 0.8476 (m-30) cc_final: 0.8268 (m-30) REVERT: E 55 ASP cc_start: 0.7747 (t0) cc_final: 0.7260 (t0) REVERT: E 70 LEU cc_start: 0.6518 (mt) cc_final: 0.5978 (tt) REVERT: E 103 SER cc_start: 0.7713 (m) cc_final: 0.7422 (p) REVERT: J 3 GLN cc_start: 0.6030 (pp30) cc_final: 0.5372 (mp10) REVERT: J 4 MET cc_start: 0.6820 (ttm) cc_final: 0.6452 (ttt) REVERT: J 18 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.6963 (ttm110) REVERT: J 44 ILE cc_start: 0.5426 (mt) cc_final: 0.5137 (mt) REVERT: J 46 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5869 (mp) REVERT: K 18 ARG cc_start: 0.7254 (ttt90) cc_final: 0.6900 (ttm110) REVERT: K 30 SER cc_start: 0.7712 (t) cc_final: 0.6989 (m) REVERT: H 20 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7962 (tp) REVERT: H 103 SER cc_start: 0.7792 (m) cc_final: 0.7394 (p) REVERT: L 24 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7919 (mtp85) outliers start: 84 outliers final: 59 residues processed: 385 average time/residue: 0.2841 time to fit residues: 165.4678 Evaluate side-chains 370 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 122 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 75 GLN B 26 HIS B 28 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 96 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN J 34 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.131865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.115892 restraints weight = 41453.344| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.76 r_work: 0.3804 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 17912 Z= 0.305 Angle : 0.851 11.854 24320 Z= 0.441 Chirality : 0.050 0.329 2757 Planarity : 0.005 0.054 3065 Dihedral : 9.683 76.403 3228 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.57 % Favored : 89.34 % Rotamer: Outliers : 5.32 % Allowed : 19.76 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.54 (0.17), residues: 2139 helix: -0.53 (0.27), residues: 336 sheet: -1.38 (0.21), residues: 579 loop : -2.24 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 36 HIS 0.011 0.002 HIS G 18 PHE 0.022 0.002 PHE C 148 TYR 0.027 0.003 TYR G 98 ARG 0.006 0.001 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 2.80079 ( 12) link_ALPHA1-6 : bond 0.01207 ( 6) link_ALPHA1-6 : angle 1.93615 ( 18) link_BETA1-4 : bond 0.00544 ( 18) link_BETA1-4 : angle 1.59411 ( 54) link_ALPHA1-3 : bond 0.01229 ( 6) link_ALPHA1-3 : angle 2.20985 ( 18) hydrogen bonds : bond 0.05347 ( 516) hydrogen bonds : angle 6.47136 ( 1407) SS BOND : bond 0.00906 ( 21) SS BOND : angle 2.15760 ( 42) covalent geometry : bond 0.00684 (17857) covalent geometry : angle 0.83912 (24176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 315 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7236 (t0) cc_final: 0.6799 (t0) REVERT: A 75 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 225 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7245 (t0) REVERT: B 122 THR cc_start: 0.8604 (m) cc_final: 0.8363 (m) REVERT: B 128 GLU cc_start: 0.5182 (tt0) cc_final: 0.4283 (tp30) REVERT: B 133 MET cc_start: 0.5130 (tpt) cc_final: 0.4639 (tpt) REVERT: C 79 PHE cc_start: 0.8043 (m-10) cc_final: 0.7163 (m-80) REVERT: C 104 ASP cc_start: 0.8850 (t0) cc_final: 0.8315 (t70) REVERT: C 119 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: C 172 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6898 (mp0) REVERT: C 320 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.6727 (ppp) REVERT: D 26 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.6774 (p90) REVERT: D 32 ARG cc_start: 0.7329 (ptp-170) cc_final: 0.6595 (ptp-170) REVERT: D 37 ASP cc_start: 0.8330 (t0) cc_final: 0.7974 (t70) REVERT: D 69 GLU cc_start: 0.7952 (tt0) cc_final: 0.7575 (pt0) REVERT: D 128 GLU cc_start: 0.6254 (tm-30) cc_final: 0.5042 (tt0) REVERT: D 137 CYS cc_start: 0.6866 (OUTLIER) cc_final: 0.5873 (p) REVERT: G 311 HIS cc_start: 0.7970 (m90) cc_final: 0.7626 (m90) REVERT: I 17 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5729 (mmp) REVERT: I 69 GLU cc_start: 0.7961 (tt0) cc_final: 0.7472 (pt0) REVERT: I 90 ASP cc_start: 0.8488 (m-30) cc_final: 0.8261 (m-30) REVERT: E 36 TRP cc_start: 0.7090 (m100) cc_final: 0.6545 (m-10) REVERT: E 55 ASP cc_start: 0.7822 (t0) cc_final: 0.7426 (t0) REVERT: E 70 LEU cc_start: 0.6838 (mt) cc_final: 0.6231 (tt) REVERT: E 103 SER cc_start: 0.7863 (m) cc_final: 0.7597 (p) REVERT: J 24 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7889 (mtp85) REVERT: J 46 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6116 (mp) REVERT: K 4 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7675 (tmt) REVERT: K 18 ARG cc_start: 0.7319 (ttt90) cc_final: 0.6930 (ttm110) REVERT: K 63 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7044 (m) REVERT: H 20 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8141 (tp) REVERT: H 55 ASP cc_start: 0.8251 (t0) cc_final: 0.8008 (t0) REVERT: H 103 SER cc_start: 0.7927 (m) cc_final: 0.7532 (p) outliers start: 100 outliers final: 70 residues processed: 381 average time/residue: 0.2827 time to fit residues: 165.1875 Evaluate side-chains 378 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 75 GLN B 26 HIS B 28 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN C 75 GLN C 96 ASN C 250 ASN C 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.117167 restraints weight = 41205.126| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.74 r_work: 0.3835 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 17912 Z= 0.234 Angle : 0.794 10.443 24320 Z= 0.409 Chirality : 0.048 0.281 2757 Planarity : 0.005 0.052 3065 Dihedral : 9.265 72.022 3228 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.65 % Favored : 91.30 % Rotamer: Outliers : 5.06 % Allowed : 21.73 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.53 (0.17), residues: 2139 helix: -0.43 (0.26), residues: 336 sheet: -1.49 (0.20), residues: 609 loop : -2.19 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP H 36 HIS 0.012 0.001 HIS B 26 PHE 0.032 0.002 PHE D 63 TYR 0.025 0.002 TYR C 98 ARG 0.006 0.001 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 4) link_NAG-ASN : angle 2.63887 ( 12) link_ALPHA1-6 : bond 0.01114 ( 6) link_ALPHA1-6 : angle 1.91975 ( 18) link_BETA1-4 : bond 0.00435 ( 18) link_BETA1-4 : angle 1.48966 ( 54) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 2.15830 ( 18) hydrogen bonds : bond 0.05020 ( 516) hydrogen bonds : angle 6.41097 ( 1407) SS BOND : bond 0.00849 ( 21) SS BOND : angle 2.49889 ( 42) covalent geometry : bond 0.00528 (17857) covalent geometry : angle 0.78017 (24176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 324 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7177 (t0) cc_final: 0.6818 (t0) REVERT: A 50 GLU cc_start: 0.7998 (tp30) cc_final: 0.7665 (tp30) REVERT: A 75 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: A 120 PHE cc_start: 0.7798 (t80) cc_final: 0.7569 (t80) REVERT: A 150 ARG cc_start: 0.7024 (mmp80) cc_final: 0.6398 (mmp80) REVERT: A 225 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7174 (t0) REVERT: B 122 THR cc_start: 0.8597 (m) cc_final: 0.8344 (m) REVERT: B 128 GLU cc_start: 0.5058 (tt0) cc_final: 0.4197 (tp30) REVERT: B 133 MET cc_start: 0.5070 (tpt) cc_final: 0.4644 (tpt) REVERT: C 79 PHE cc_start: 0.7975 (m-10) cc_final: 0.7086 (m-80) REVERT: C 104 ASP cc_start: 0.8812 (t0) cc_final: 0.8256 (t70) REVERT: C 119 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: C 172 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6787 (mp0) REVERT: C 225 ASP cc_start: 0.7193 (t0) cc_final: 0.6956 (t0) REVERT: C 320 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.6783 (ppp) REVERT: D 32 ARG cc_start: 0.7261 (ptp-170) cc_final: 0.6657 (ptp-170) REVERT: D 37 ASP cc_start: 0.8273 (t0) cc_final: 0.7883 (t70) REVERT: D 42 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7891 (tp-100) REVERT: D 69 GLU cc_start: 0.7941 (tt0) cc_final: 0.7525 (pt0) REVERT: D 122 THR cc_start: 0.8225 (m) cc_final: 0.7934 (m) REVERT: D 123 LYS cc_start: 0.7582 (tttt) cc_final: 0.7244 (tttm) REVERT: D 128 GLU cc_start: 0.6285 (tm-30) cc_final: 0.5041 (tt0) REVERT: D 137 CYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6985 (m) REVERT: G 17 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7447 (m170) REVERT: G 311 HIS cc_start: 0.7974 (m90) cc_final: 0.7599 (m90) REVERT: I 17 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5431 (mmp) REVERT: I 69 GLU cc_start: 0.7988 (tt0) cc_final: 0.7477 (pt0) REVERT: I 90 ASP cc_start: 0.8488 (m-30) cc_final: 0.8265 (m-30) REVERT: E 55 ASP cc_start: 0.7802 (t0) cc_final: 0.7401 (t0) REVERT: E 70 LEU cc_start: 0.6893 (mt) cc_final: 0.6220 (tt) REVERT: E 103 SER cc_start: 0.7813 (m) cc_final: 0.7573 (p) REVERT: J 3 GLN cc_start: 0.5800 (pp30) cc_final: 0.5130 (mp10) REVERT: J 24 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7201 (mtp85) REVERT: J 30 SER cc_start: 0.7999 (t) cc_final: 0.7308 (m) REVERT: J 44 ILE cc_start: 0.5381 (mt) cc_final: 0.5115 (mt) REVERT: J 46 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5969 (mp) REVERT: K 18 ARG cc_start: 0.7307 (ttt90) cc_final: 0.6916 (ttm110) REVERT: K 30 SER cc_start: 0.7958 (t) cc_final: 0.7238 (m) REVERT: K 44 ILE cc_start: 0.5888 (mt) cc_final: 0.5430 (mt) REVERT: H 55 ASP cc_start: 0.8273 (t0) cc_final: 0.7993 (t0) REVERT: H 81 MET cc_start: 0.5807 (mtp) cc_final: 0.5114 (mtp) REVERT: H 103 SER cc_start: 0.7829 (m) cc_final: 0.7278 (t) REVERT: L 96 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4147 (mtm-85) outliers start: 95 outliers final: 66 residues processed: 387 average time/residue: 0.2733 time to fit residues: 160.7249 Evaluate side-chains 384 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 309 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 ARG Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 96 ASN C 250 ASN C 296 ASN D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN K 34 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.132605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.116553 restraints weight = 41548.301| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.75 r_work: 0.3826 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17912 Z= 0.239 Angle : 0.808 12.356 24320 Z= 0.416 Chirality : 0.048 0.278 2757 Planarity : 0.005 0.053 3065 Dihedral : 9.084 69.519 3228 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 4.69 % Allowed : 22.26 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.56 (0.17), residues: 2139 helix: -0.46 (0.27), residues: 336 sheet: -1.47 (0.21), residues: 603 loop : -2.24 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.004 TRP K 35 HIS 0.013 0.002 HIS B 26 PHE 0.032 0.002 PHE D 63 TYR 0.026 0.002 TYR C 98 ARG 0.010 0.001 ARG F 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 2.59062 ( 12) link_ALPHA1-6 : bond 0.01159 ( 6) link_ALPHA1-6 : angle 1.87502 ( 18) link_BETA1-4 : bond 0.00453 ( 18) link_BETA1-4 : angle 1.46578 ( 54) link_ALPHA1-3 : bond 0.01109 ( 6) link_ALPHA1-3 : angle 2.10540 ( 18) hydrogen bonds : bond 0.05039 ( 516) hydrogen bonds : angle 6.39005 ( 1407) SS BOND : bond 0.00761 ( 21) SS BOND : angle 2.09930 ( 42) covalent geometry : bond 0.00538 (17857) covalent geometry : angle 0.79649 (24176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 311 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7118 (t0) cc_final: 0.6740 (t0) REVERT: A 50 GLU cc_start: 0.7974 (tp30) cc_final: 0.7587 (tp30) REVERT: A 75 GLN cc_start: 0.7540 (tp40) cc_final: 0.7223 (tt0) REVERT: A 120 PHE cc_start: 0.7838 (t80) cc_final: 0.7564 (t80) REVERT: A 150 ARG cc_start: 0.7063 (mmp80) cc_final: 0.6380 (mmp80) REVERT: A 225 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 122 THR cc_start: 0.8572 (m) cc_final: 0.8316 (m) REVERT: B 128 GLU cc_start: 0.5123 (tt0) cc_final: 0.4330 (tp30) REVERT: B 133 MET cc_start: 0.5157 (tpt) cc_final: 0.4693 (tpt) REVERT: C 104 ASP cc_start: 0.8724 (t0) cc_final: 0.8211 (t0) REVERT: C 119 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 164 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 172 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6835 (mp0) REVERT: C 225 ASP cc_start: 0.7240 (t0) cc_final: 0.6987 (t0) REVERT: C 259 LYS cc_start: 0.8819 (tttt) cc_final: 0.8426 (ttpp) REVERT: C 320 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.6867 (ppp) REVERT: D 26 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.6791 (p90) REVERT: D 32 ARG cc_start: 0.7298 (ptp-170) cc_final: 0.6536 (ptp-170) REVERT: D 37 ASP cc_start: 0.8255 (t0) cc_final: 0.7883 (t70) REVERT: D 69 GLU cc_start: 0.7837 (tt0) cc_final: 0.7367 (pt0) REVERT: D 122 THR cc_start: 0.8215 (m) cc_final: 0.7939 (m) REVERT: D 123 LYS cc_start: 0.7618 (tttt) cc_final: 0.7319 (tttm) REVERT: D 128 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5087 (tt0) REVERT: D 141 TYR cc_start: 0.6210 (t80) cc_final: 0.5902 (t80) REVERT: G 17 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7455 (m170) REVERT: I 17 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5501 (mmp) REVERT: I 69 GLU cc_start: 0.7990 (tt0) cc_final: 0.7534 (pt0) REVERT: I 90 ASP cc_start: 0.8451 (m-30) cc_final: 0.8228 (m-30) REVERT: E 55 ASP cc_start: 0.7840 (t0) cc_final: 0.7463 (t0) REVERT: E 70 LEU cc_start: 0.7143 (mt) cc_final: 0.6494 (tt) REVERT: E 103 SER cc_start: 0.7846 (m) cc_final: 0.7607 (p) REVERT: J 3 GLN cc_start: 0.5489 (pp30) cc_final: 0.5101 (mp10) REVERT: J 24 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7929 (mtp85) REVERT: J 30 SER cc_start: 0.8077 (t) cc_final: 0.7413 (m) REVERT: J 44 ILE cc_start: 0.5470 (mt) cc_final: 0.5207 (mt) REVERT: K 18 ARG cc_start: 0.7093 (ttt90) cc_final: 0.6822 (ttm110) REVERT: K 30 SER cc_start: 0.7966 (t) cc_final: 0.7292 (m) REVERT: H 55 ASP cc_start: 0.8355 (t0) cc_final: 0.8118 (t0) REVERT: H 81 MET cc_start: 0.5954 (mtp) cc_final: 0.5168 (mtp) REVERT: H 103 SER cc_start: 0.7878 (m) cc_final: 0.7657 (t) REVERT: L 89 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4121 (pp30) outliers start: 88 outliers final: 70 residues processed: 370 average time/residue: 0.2828 time to fit residues: 159.6032 Evaluate side-chains 374 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 ARG Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 157 optimal weight: 0.0670 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 96 ASN C 296 ASN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN E 1 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.136633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120626 restraints weight = 40705.870| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.76 r_work: 0.3886 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17912 Z= 0.151 Angle : 0.747 10.931 24320 Z= 0.384 Chirality : 0.046 0.254 2757 Planarity : 0.005 0.052 3065 Dihedral : 8.475 63.391 3228 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.29 % Favored : 92.66 % Rotamer: Outliers : 3.51 % Allowed : 24.01 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.44 (0.17), residues: 2139 helix: -0.17 (0.27), residues: 336 sheet: -1.59 (0.20), residues: 639 loop : -2.10 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP L 35 HIS 0.007 0.001 HIS B 26 PHE 0.033 0.002 PHE C 120 TYR 0.022 0.002 TYR C 98 ARG 0.008 0.001 ARG F 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 4) link_NAG-ASN : angle 2.13594 ( 12) link_ALPHA1-6 : bond 0.00932 ( 6) link_ALPHA1-6 : angle 1.86899 ( 18) link_BETA1-4 : bond 0.00368 ( 18) link_BETA1-4 : angle 1.41705 ( 54) link_ALPHA1-3 : bond 0.01022 ( 6) link_ALPHA1-3 : angle 2.06530 ( 18) hydrogen bonds : bond 0.04500 ( 516) hydrogen bonds : angle 6.25644 ( 1407) SS BOND : bond 0.00557 ( 21) SS BOND : angle 2.13231 ( 42) covalent geometry : bond 0.00336 (17857) covalent geometry : angle 0.73574 (24176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 336 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7034 (t0) cc_final: 0.6723 (t0) REVERT: A 150 ARG cc_start: 0.6835 (mmp80) cc_final: 0.6371 (mmp80) REVERT: A 225 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 261 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7754 (ptp-110) REVERT: B 46 ASP cc_start: 0.8213 (m-30) cc_final: 0.7830 (m-30) REVERT: B 122 THR cc_start: 0.8487 (m) cc_final: 0.8225 (m) REVERT: B 128 GLU cc_start: 0.5070 (tt0) cc_final: 0.4289 (tp30) REVERT: B 133 MET cc_start: 0.5063 (tpt) cc_final: 0.4672 (tpt) REVERT: C 75 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6651 (tp40) REVERT: C 104 ASP cc_start: 0.8621 (t0) cc_final: 0.8032 (t70) REVERT: C 225 ASP cc_start: 0.7180 (t0) cc_final: 0.6948 (t0) REVERT: C 259 LYS cc_start: 0.8757 (tttt) cc_final: 0.8357 (ttpp) REVERT: C 320 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.6980 (ppp) REVERT: D 32 ARG cc_start: 0.6990 (ptp-170) cc_final: 0.6501 (ptp-170) REVERT: D 37 ASP cc_start: 0.8193 (t0) cc_final: 0.7803 (t70) REVERT: D 69 GLU cc_start: 0.7832 (tt0) cc_final: 0.7335 (pt0) REVERT: D 122 THR cc_start: 0.8127 (m) cc_final: 0.7854 (m) REVERT: D 123 LYS cc_start: 0.7489 (tttt) cc_final: 0.7181 (tttm) REVERT: D 128 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5037 (tt0) REVERT: D 141 TYR cc_start: 0.6018 (t80) cc_final: 0.5758 (t80) REVERT: G 17 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6927 (m170) REVERT: G 311 HIS cc_start: 0.7889 (m90) cc_final: 0.7524 (m90) REVERT: G 320 MET cc_start: 0.8688 (ppp) cc_final: 0.8428 (ppp) REVERT: I 17 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.4841 (mmt) REVERT: I 69 GLU cc_start: 0.7952 (tt0) cc_final: 0.7511 (pt0) REVERT: I 90 ASP cc_start: 0.8412 (m-30) cc_final: 0.7907 (m-30) REVERT: E 55 ASP cc_start: 0.7775 (t0) cc_final: 0.7404 (t0) REVERT: E 103 SER cc_start: 0.7706 (m) cc_final: 0.7468 (p) REVERT: J 30 SER cc_start: 0.7999 (t) cc_final: 0.7356 (m) REVERT: J 46 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5835 (mp) REVERT: F 65 LYS cc_start: 0.7237 (pttm) cc_final: 0.6996 (pttm) REVERT: F 70 LEU cc_start: 0.7449 (mt) cc_final: 0.7142 (tt) REVERT: F 101 TYR cc_start: 0.6066 (t80) cc_final: 0.5617 (t80) REVERT: K 18 ARG cc_start: 0.7051 (ttt90) cc_final: 0.6812 (ttm110) REVERT: K 30 SER cc_start: 0.7937 (t) cc_final: 0.7254 (m) REVERT: H 81 MET cc_start: 0.5997 (mtp) cc_final: 0.5223 (mtp) REVERT: H 103 SER cc_start: 0.7710 (m) cc_final: 0.7482 (t) REVERT: L 18 ARG cc_start: 0.7258 (ttt-90) cc_final: 0.6951 (ttm110) REVERT: L 89 GLN cc_start: 0.5535 (OUTLIER) cc_final: 0.4678 (pp30) outliers start: 66 outliers final: 47 residues processed: 375 average time/residue: 0.2903 time to fit residues: 166.5102 Evaluate side-chains 364 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN E 1 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.116408 restraints weight = 41334.855| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.73 r_work: 0.3823 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17912 Z= 0.244 Angle : 0.818 11.109 24320 Z= 0.422 Chirality : 0.048 0.271 2757 Planarity : 0.005 0.054 3065 Dihedral : 8.628 61.730 3228 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.29 % Favored : 89.67 % Rotamer: Outliers : 3.83 % Allowed : 23.80 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.45 (0.17), residues: 2139 helix: -0.26 (0.27), residues: 336 sheet: -1.49 (0.21), residues: 603 loop : -2.15 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.004 TRP E 36 HIS 0.011 0.002 HIS B 26 PHE 0.028 0.002 PHE D 63 TYR 0.024 0.002 TYR G 98 ARG 0.008 0.001 ARG F 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 4) link_NAG-ASN : angle 2.40578 ( 12) link_ALPHA1-6 : bond 0.01061 ( 6) link_ALPHA1-6 : angle 1.79517 ( 18) link_BETA1-4 : bond 0.00528 ( 18) link_BETA1-4 : angle 1.43690 ( 54) link_ALPHA1-3 : bond 0.00996 ( 6) link_ALPHA1-3 : angle 1.96422 ( 18) hydrogen bonds : bond 0.04933 ( 516) hydrogen bonds : angle 6.34541 ( 1407) SS BOND : bond 0.00849 ( 21) SS BOND : angle 2.26110 ( 42) covalent geometry : bond 0.00548 (17857) covalent geometry : angle 0.80756 (24176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9052.27 seconds wall clock time: 160 minutes 36.03 seconds (9636.03 seconds total)