Starting phenix.real_space_refine on Sun Aug 24 05:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txu_41705/08_2025/8txu_41705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txu_41705/08_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_41705/08_2025/8txu_41705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txu_41705/08_2025/8txu_41705.map" model { file = "/net/cci-nas-00/data/ceres_data/8txu_41705/08_2025/8txu_41705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txu_41705/08_2025/8txu_41705.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.53, per 1000 atoms: 0.26 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: 1.79 Conformation dependent library (CDL) restraints added in 753.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.75 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: 3.16 Time building geometry restraints manager: 2.29 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: 3.890 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- 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 : 7.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 229 TYR 0.027 0.002 TYR B 141 PHE 0.034 0.002 PHE I 9 TRP 0.030 0.002 TRP B 14 HIS 0.013 0.002 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00511 (17857) covalent geometry : angle 0.93695 (24176) SS BOND : bond 0.00420 ( 21) SS BOND : angle 1.79383 ( 42) hydrogen bonds : bond 0.21509 ( 516) hydrogen bonds : angle 8.79583 ( 1407) link_ALPHA1-3 : bond 0.00364 ( 6) link_ALPHA1-3 : angle 1.52798 ( 18) 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_NAG-ASN : bond 0.00886 ( 4) link_NAG-ASN : angle 4.00993 ( 12) *********************** 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 : 0.698 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: 0.7060 (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: 0.6503 (m-10) REVERT: C 276 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7193 (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: 0.6963 (pt0) REVERT: D 128 GLU cc_start: 0.5692 (tm-30) cc_final: 0.4752 (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: 0.5805 (p0) REVERT: G 262 SER cc_start: 0.8589 (t) cc_final: 0.8377 (p) REVERT: G 276 LYS cc_start: 0.7386 (mmtm) cc_final: 0.7151 (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: 0.6958 (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: 0.6573 (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: 0.6127 (t) REVERT: J 74 THR cc_start: 0.7637 (m) cc_final: 0.7433 (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: 0.1458 time to fit residues: 131.6704 Evaluate side-chains 365 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 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** C 156 HIS C 197 GLN C 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4384 r_free = 0.4384 target = 0.150559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.135401 restraints weight = 41077.921| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.82 r_work: 0.4082 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17912 Z= 0.159 Angle : 0.714 7.593 24320 Z= 0.368 Chirality : 0.047 0.273 2757 Planarity : 0.005 0.075 3065 Dihedral : 13.348 90.315 3228 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.09 % Allowed : 13.53 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.18), residues: 2139 helix: 0.40 (0.28), residues: 321 sheet: -1.04 (0.21), residues: 636 loop : -1.77 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 69 TYR 0.035 0.002 TYR H 101 PHE 0.017 0.002 PHE C 148 TRP 0.027 0.002 TRP F 36 HIS 0.008 0.002 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00348 (17857) covalent geometry : angle 0.69922 (24176) SS BOND : bond 0.00442 ( 21) SS BOND : angle 1.27084 ( 42) hydrogen bonds : bond 0.04600 ( 516) hydrogen bonds : angle 6.31308 ( 1407) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 3.12671 ( 18) link_ALPHA1-6 : bond 0.00699 ( 6) link_ALPHA1-6 : angle 1.83012 ( 18) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 2.00600 ( 54) link_NAG-ASN : bond 0.00764 ( 4) link_NAG-ASN : angle 2.27108 ( 12) *********************** 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 460 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 402 time to evaluate : 0.700 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: 0.6463 (t0) cc_final: 0.6156 (t0) REVERT: A 191 GLN cc_start: 0.5464 (tt0) cc_final: 0.5052 (tt0) REVERT: A 259 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8428 (ttmm) REVERT: A 262 SER cc_start: 0.8731 (m) cc_final: 0.8278 (p) REVERT: B 67 GLU cc_start: 0.7933 (mm-30) cc_final: 0.6683 (tt0) REVERT: B 128 GLU cc_start: 0.4921 (tt0) cc_final: 0.3621 (tp30) REVERT: B 133 MET cc_start: 0.4409 (tpt) cc_final: 0.4130 (tpt) REVERT: C 79 PHE cc_start: 0.7516 (m-10) cc_final: 0.6635 (m-10) REVERT: C 172 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6304 (mp0) REVERT: C 276 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7307 (mmmt) REVERT: D 69 GLU cc_start: 0.7849 (tt0) cc_final: 0.7369 (pt0) REVERT: D 123 LYS cc_start: 0.7751 (tptt) cc_final: 0.7367 (pptt) REVERT: D 128 GLU cc_start: 0.5951 (tm-30) cc_final: 0.4929 (tt0) REVERT: D 133 MET cc_start: 0.3849 (tmm) cc_final: 0.2985 (tpt) REVERT: G 188 ASP cc_start: 0.6302 (t0) cc_final: 0.5833 (p0) REVERT: G 276 LYS cc_start: 0.7467 (mmtm) cc_final: 0.7233 (mmmt) REVERT: I 67 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6804 (tt0) REVERT: I 69 GLU cc_start: 0.7511 (tt0) cc_final: 0.6905 (pt0) REVERT: I 90 ASP cc_start: 0.8379 (m-30) cc_final: 0.7980 (m-30) REVERT: E 36 TRP cc_start: 0.6965 (m100) cc_final: 0.6604 (m100) REVERT: E 43 GLN cc_start: 0.5550 (mt0) cc_final: 0.4919 (mt0) REVERT: E 55 ASP cc_start: 0.7556 (t0) cc_final: 0.7257 (t0) REVERT: E 67 LYS cc_start: 0.5734 (tmtt) cc_final: 0.5224 (tptm) REVERT: E 81 MET cc_start: 0.4933 (OUTLIER) cc_final: 0.3877 (mtp) REVERT: E 103 SER cc_start: 0.7274 (m) cc_final: 0.6991 (p) REVERT: J 3 GLN cc_start: 0.6123 (pp30) cc_final: 0.5502 (mp10) REVERT: J 4 MET cc_start: 0.7036 (ttm) cc_final: 0.6513 (ttt) REVERT: J 18 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.6941 (ttm170) REVERT: F 55 ASP cc_start: 0.7861 (t0) cc_final: 0.7631 (t0) REVERT: F 69 ARG cc_start: 0.6950 (ptp-170) cc_final: 0.6167 (ptp-170) REVERT: F 80 TYR cc_start: 0.5650 (m-80) cc_final: 0.5335 (m-80) REVERT: K 18 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7263 (ttm170) REVERT: H 28 THR cc_start: 0.7491 (m) cc_final: 0.6829 (p) REVERT: H 32 TYR cc_start: 0.8168 (m-80) cc_final: 0.7815 (m-80) REVERT: H 36 TRP cc_start: 0.7035 (m100) cc_final: 0.6714 (m100) REVERT: H 55 ASP cc_start: 0.7764 (t0) cc_final: 0.7540 (t0) REVERT: H 81 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.3880 (mtp) REVERT: H 103 SER cc_start: 0.7570 (m) cc_final: 0.7111 (p) REVERT: L 31 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7772 (t0) REVERT: L 34 ASN cc_start: 0.8030 (m-40) cc_final: 0.7386 (m-40) REVERT: L 54 LEU cc_start: 0.5985 (tp) cc_final: 0.5405 (pt) REVERT: L 86 TYR cc_start: 0.6167 (m-80) cc_final: 0.5846 (m-80) outliers start: 58 outliers final: 38 residues processed: 433 average time/residue: 0.1374 time to fit residues: 90.4263 Evaluate side-chains 386 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 SER 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 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 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 G residue 270 SER 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 81 MET 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 88 CYS 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 6 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.0020 chunk 127 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- 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 ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 8 ASN ** 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** E 61 ASN J 31 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN K 3 GLN H 1 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.143825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.128138 restraints weight = 41214.039| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.84 r_work: 0.3981 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17912 Z= 0.206 Angle : 0.728 10.182 24320 Z= 0.375 Chirality : 0.048 0.315 2757 Planarity : 0.005 0.064 3065 Dihedral : 11.550 89.530 3228 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.21 % Allowed : 15.34 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.18), residues: 2139 helix: 0.12 (0.27), residues: 333 sheet: -1.12 (0.21), residues: 597 loop : -1.82 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.032 0.002 TYR C 195 PHE 0.019 0.002 PHE C 148 TRP 0.020 0.002 TRP F 36 HIS 0.009 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00460 (17857) covalent geometry : angle 0.71783 (24176) SS BOND : bond 0.00480 ( 21) SS BOND : angle 1.47033 ( 42) hydrogen bonds : bond 0.04711 ( 516) hydrogen bonds : angle 5.97452 ( 1407) link_ALPHA1-3 : bond 0.01103 ( 6) link_ALPHA1-3 : angle 2.03713 ( 18) link_ALPHA1-6 : bond 0.00954 ( 6) link_ALPHA1-6 : angle 1.89227 ( 18) link_BETA1-4 : bond 0.00564 ( 18) link_BETA1-4 : angle 1.64721 ( 54) link_NAG-ASN : bond 0.00483 ( 4) link_NAG-ASN : angle 2.33457 ( 12) *********************** 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 439 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 360 time to evaluate : 0.717 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: A 22 ASN cc_start: 0.6741 (t0) cc_final: 0.6390 (t0) REVERT: A 75 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: A 187 THR cc_start: 0.6961 (p) cc_final: 0.6753 (p) REVERT: A 245 ILE cc_start: 0.8628 (mm) cc_final: 0.8311 (mm) REVERT: A 262 SER cc_start: 0.8813 (m) cc_final: 0.8287 (p) REVERT: B 32 ARG cc_start: 0.6746 (ptm160) cc_final: 0.5954 (ptm-80) REVERT: B 128 GLU cc_start: 0.4923 (tt0) cc_final: 0.3802 (tp30) REVERT: B 133 MET cc_start: 0.4772 (tpt) cc_final: 0.4370 (tpt) REVERT: C 79 PHE cc_start: 0.7586 (m-10) cc_final: 0.6662 (m-10) REVERT: C 159 TYR cc_start: 0.5947 (m-10) cc_final: 0.5733 (m-10) REVERT: C 172 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6475 (mp0) REVERT: D 37 ASP cc_start: 0.7909 (t0) cc_final: 0.7632 (t70) REVERT: D 69 GLU cc_start: 0.7895 (tt0) cc_final: 0.7374 (pt0) REVERT: D 128 GLU cc_start: 0.6038 (tm-30) cc_final: 0.4925 (tt0) REVERT: D 133 MET cc_start: 0.4368 (tmm) cc_final: 0.3452 (tpt) REVERT: G 22 ASN cc_start: 0.7563 (m110) cc_final: 0.7096 (p0) REVERT: G 276 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7437 (mmmt) REVERT: I 37 ASP cc_start: 0.6911 (t70) cc_final: 0.6374 (t70) REVERT: I 67 GLU cc_start: 0.7916 (mm-30) cc_final: 0.6766 (tt0) REVERT: I 69 GLU cc_start: 0.7699 (tt0) cc_final: 0.7215 (pt0) REVERT: I 90 ASP cc_start: 0.8380 (m-30) cc_final: 0.7975 (m-30) REVERT: E 36 TRP cc_start: 0.7183 (m100) cc_final: 0.6859 (m100) REVERT: E 43 GLN cc_start: 0.5399 (mt0) cc_final: 0.5135 (mt0) REVERT: E 55 ASP cc_start: 0.7701 (t0) cc_final: 0.7288 (t0) REVERT: E 81 MET cc_start: 0.5084 (mtp) cc_final: 0.4756 (mtp) REVERT: E 103 SER cc_start: 0.7503 (m) cc_final: 0.7236 (p) REVERT: J 3 GLN cc_start: 0.6032 (pp30) cc_final: 0.5496 (mp10) REVERT: J 18 ARG cc_start: 0.7665 (ttt-90) cc_final: 0.7021 (ttm110) REVERT: F 4 LEU cc_start: 0.6808 (mt) cc_final: 0.6547 (mp) REVERT: F 80 TYR cc_start: 0.6037 (m-80) cc_final: 0.5589 (m-80) REVERT: K 18 ARG cc_start: 0.7451 (ttt90) cc_final: 0.7100 (ttm110) REVERT: K 74 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7895 (p) REVERT: H 28 THR cc_start: 0.7496 (m) cc_final: 0.6892 (p) REVERT: H 36 TRP cc_start: 0.7065 (m100) cc_final: 0.6725 (m100) REVERT: H 55 ASP cc_start: 0.7967 (t0) cc_final: 0.7608 (t0) REVERT: H 81 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4419 (mtp) REVERT: H 103 SER cc_start: 0.7803 (m) cc_final: 0.7368 (p) REVERT: L 31 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7855 (t0) REVERT: L 54 LEU cc_start: 0.6092 (tp) cc_final: 0.5531 (pt) outliers start: 79 outliers final: 49 residues processed: 402 average time/residue: 0.1373 time to fit residues: 84.6800 Evaluate side-chains 370 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 43 VAL 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 167 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 C residue 204 VAL 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 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 28 ASN Chi-restraints excluded: chain I residue 112 ASP 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 115 THR 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 4 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU 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 20 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR 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 63 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 47 GLN ** 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** K 3 GLN H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.138216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.122177 restraints weight = 41296.959| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.82 r_work: 0.3901 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17912 Z= 0.251 Angle : 0.780 10.089 24320 Z= 0.401 Chirality : 0.049 0.348 2757 Planarity : 0.005 0.060 3065 Dihedral : 10.317 84.616 3228 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.11 % Allowed : 18.00 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.17), residues: 2139 helix: 0.06 (0.27), residues: 333 sheet: -1.33 (0.21), residues: 606 loop : -1.97 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 40 TYR 0.024 0.002 TYR G 98 PHE 0.018 0.002 PHE C 148 TRP 0.035 0.003 TRP F 36 HIS 0.011 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00562 (17857) covalent geometry : angle 0.76821 (24176) SS BOND : bond 0.00708 ( 21) SS BOND : angle 1.64797 ( 42) hydrogen bonds : bond 0.04781 ( 516) hydrogen bonds : angle 6.14322 ( 1407) link_ALPHA1-3 : bond 0.00999 ( 6) link_ALPHA1-3 : angle 2.33386 ( 18) link_ALPHA1-6 : bond 0.01186 ( 6) link_ALPHA1-6 : angle 2.03470 ( 18) link_BETA1-4 : bond 0.00482 ( 18) link_BETA1-4 : angle 1.65922 ( 54) link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 2.54201 ( 12) *********************** 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 425 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 329 time to evaluate : 0.742 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: 0.7038 (t0) cc_final: 0.6621 (t0) REVERT: A 75 GLN cc_start: 0.7785 (tp-100) cc_final: 0.7542 (tp40) REVERT: A 187 THR cc_start: 0.7103 (p) cc_final: 0.6886 (p) REVERT: B 32 ARG cc_start: 0.6826 (ptm160) cc_final: 0.6345 (ptp-170) REVERT: B 128 GLU cc_start: 0.5012 (tt0) cc_final: 0.3979 (tp30) REVERT: B 133 MET cc_start: 0.5057 (tpt) cc_final: 0.4663 (tpt) REVERT: C 79 PHE cc_start: 0.7732 (m-10) cc_final: 0.6640 (m-80) REVERT: C 119 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: C 159 TYR cc_start: 0.6180 (m-10) cc_final: 0.5953 (m-10) REVERT: C 172 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6627 (mp0) REVERT: D 9 PHE cc_start: 0.7119 (p90) cc_final: 0.6755 (p90) REVERT: D 37 ASP cc_start: 0.8126 (t0) cc_final: 0.7735 (t70) REVERT: D 42 GLN cc_start: 0.8376 (tp40) cc_final: 0.8047 (mm-40) REVERT: D 69 GLU cc_start: 0.7909 (tt0) cc_final: 0.7479 (pt0) REVERT: D 128 GLU cc_start: 0.6319 (tm-30) cc_final: 0.5169 (tt0) REVERT: I 69 GLU cc_start: 0.7758 (tt0) cc_final: 0.7435 (pt0) REVERT: I 90 ASP cc_start: 0.8472 (m-30) cc_final: 0.8059 (m-30) REVERT: E 36 TRP cc_start: 0.7248 (m100) cc_final: 0.6763 (m100) REVERT: E 43 GLN cc_start: 0.5707 (mt0) cc_final: 0.5455 (mt0) REVERT: E 55 ASP cc_start: 0.7928 (t0) cc_final: 0.7604 (t0) REVERT: E 81 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.4833 (mtp) REVERT: E 103 SER cc_start: 0.7683 (m) cc_final: 0.7401 (p) REVERT: J 3 GLN cc_start: 0.6083 (pp30) cc_final: 0.5296 (mp10) REVERT: J 18 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.6987 (ttm110) REVERT: K 18 ARG cc_start: 0.7348 (ttt90) cc_final: 0.7060 (ttm110) REVERT: K 30 SER cc_start: 0.7960 (t) cc_final: 0.7113 (m) REVERT: K 74 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7940 (p) REVERT: H 36 TRP cc_start: 0.7024 (m100) cc_final: 0.6818 (m-10) REVERT: H 55 ASP cc_start: 0.8137 (t0) cc_final: 0.7847 (t0) REVERT: H 103 SER cc_start: 0.7837 (m) cc_final: 0.7494 (p) REVERT: L 18 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.6881 (ttm110) REVERT: L 24 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7763 (mtp85) REVERT: L 31 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7921 (t0) REVERT: L 54 LEU cc_start: 0.6440 (tp) cc_final: 0.6059 (pp) outliers start: 96 outliers final: 61 residues processed: 386 average time/residue: 0.1355 time to fit residues: 80.4548 Evaluate side-chains 369 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 98 TYR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 155 THR 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 17 HIS Chi-restraints excluded: chain C residue 40 THR 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 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 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 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 28 ASN 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 E residue 20 LEU 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 4 MET Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 48 ILE 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 K residue 70 ASP 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 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 31 ASN 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 69 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 75 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.123238 restraints weight = 41189.119| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.83 r_work: 0.3914 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17912 Z= 0.181 Angle : 0.702 8.794 24320 Z= 0.361 Chirality : 0.046 0.312 2757 Planarity : 0.004 0.055 3065 Dihedral : 9.733 80.956 3228 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 5.01 % Allowed : 19.01 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.17), residues: 2139 helix: 0.13 (0.27), residues: 333 sheet: -1.19 (0.21), residues: 588 loop : -1.94 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 150 TYR 0.019 0.002 TYR D 141 PHE 0.023 0.002 PHE C 148 TRP 0.029 0.002 TRP F 36 HIS 0.010 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00403 (17857) covalent geometry : angle 0.68832 (24176) SS BOND : bond 0.00658 ( 21) SS BOND : angle 2.16590 ( 42) hydrogen bonds : bond 0.04466 ( 516) hydrogen bonds : angle 6.02690 ( 1407) link_ALPHA1-3 : bond 0.01128 ( 6) link_ALPHA1-3 : angle 2.19926 ( 18) link_ALPHA1-6 : bond 0.01038 ( 6) link_ALPHA1-6 : angle 1.96548 ( 18) link_BETA1-4 : bond 0.00420 ( 18) link_BETA1-4 : angle 1.52571 ( 54) link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 2.36582 ( 12) *********************** 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 429 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 335 time to evaluate : 0.749 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: A 22 ASN cc_start: 0.6960 (t0) cc_final: 0.6552 (t0) REVERT: A 75 GLN cc_start: 0.7661 (tp-100) cc_final: 0.7225 (tt0) REVERT: A 147 PHE cc_start: 0.5802 (t80) cc_final: 0.5495 (t80) REVERT: A 187 THR cc_start: 0.7091 (p) cc_final: 0.6872 (p) REVERT: B 128 GLU cc_start: 0.4993 (tt0) cc_final: 0.3922 (tp30) REVERT: B 133 MET cc_start: 0.5021 (tpt) cc_final: 0.4609 (tpt) REVERT: C 79 PHE cc_start: 0.7789 (m-10) cc_final: 0.6806 (m-80) REVERT: C 159 TYR cc_start: 0.6168 (m-10) cc_final: 0.5943 (m-10) REVERT: C 172 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6576 (mp0) REVERT: C 174 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.5012 (p90) REVERT: D 37 ASP cc_start: 0.8137 (t0) cc_final: 0.7664 (t70) REVERT: D 69 GLU cc_start: 0.7911 (tt0) cc_final: 0.7486 (pt0) REVERT: D 128 GLU cc_start: 0.6371 (tm-30) cc_final: 0.5215 (tt0) REVERT: D 129 ASN cc_start: 0.3852 (OUTLIER) cc_final: 0.3506 (p0) REVERT: G 17 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7284 (m170) REVERT: G 311 HIS cc_start: 0.7809 (m90) cc_final: 0.7421 (m90) REVERT: I 17 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5322 (mmp) REVERT: I 69 GLU cc_start: 0.7726 (tt0) cc_final: 0.7416 (pt0) REVERT: I 90 ASP cc_start: 0.8435 (m-30) cc_final: 0.8013 (m-30) REVERT: E 36 TRP cc_start: 0.7127 (m100) cc_final: 0.6685 (m100) REVERT: E 43 GLN cc_start: 0.5595 (mt0) cc_final: 0.4897 (mt0) REVERT: E 55 ASP cc_start: 0.7852 (t0) cc_final: 0.7457 (t0) REVERT: E 81 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.5005 (mtp) REVERT: E 103 SER cc_start: 0.7565 (m) cc_final: 0.7281 (p) REVERT: J 3 GLN cc_start: 0.6029 (pp30) cc_final: 0.5218 (mp10) REVERT: J 18 ARG cc_start: 0.7552 (ttt-90) cc_final: 0.6965 (ttm110) REVERT: J 44 ILE cc_start: 0.5495 (mt) cc_final: 0.5202 (mt) REVERT: K 18 ARG cc_start: 0.7301 (ttt90) cc_final: 0.6937 (ttm110) REVERT: K 30 SER cc_start: 0.7927 (t) cc_final: 0.7037 (m) REVERT: K 31 ASN cc_start: 0.8119 (m-40) cc_final: 0.7314 (p0) REVERT: K 44 ILE cc_start: 0.5583 (mt) cc_final: 0.5235 (mt) REVERT: H 36 TRP cc_start: 0.7044 (m100) cc_final: 0.6646 (m-10) REVERT: H 55 ASP cc_start: 0.8113 (t0) cc_final: 0.7855 (t0) REVERT: H 81 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.4024 (mtp) REVERT: H 103 SER cc_start: 0.7772 (m) cc_final: 0.7386 (p) REVERT: L 18 ARG cc_start: 0.7314 (ttt-90) cc_final: 0.6904 (ttm110) REVERT: L 31 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7811 (t0) outliers start: 94 outliers final: 64 residues processed: 393 average time/residue: 0.1357 time to fit residues: 82.1796 Evaluate side-chains 374 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 98 TYR Chi-restraints excluded: chain A residue 102 VAL 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 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 98 TYR 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 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 129 ASN 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 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 G residue 288 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 20 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 74 LYS 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 70 ASP 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 19 VAL Chi-restraints excluded: chain L residue 31 ASN 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 88 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 74 optimal weight: 0.3980 chunk 158 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 311 HIS ** 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** 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 295 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.118703 restraints weight = 41352.236| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.80 r_work: 0.3849 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17912 Z= 0.255 Angle : 0.775 10.271 24320 Z= 0.400 Chirality : 0.048 0.311 2757 Planarity : 0.005 0.055 3065 Dihedral : 9.536 78.630 3228 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.77 % Favored : 90.18 % 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 : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.17), residues: 2139 helix: -0.16 (0.27), residues: 333 sheet: -1.33 (0.21), residues: 588 loop : -2.08 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.020 0.002 TYR F 95 PHE 0.020 0.002 PHE C 148 TRP 0.030 0.003 TRP G 84 HIS 0.010 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00573 (17857) covalent geometry : angle 0.76236 (24176) SS BOND : bond 0.00725 ( 21) SS BOND : angle 2.03012 ( 42) hydrogen bonds : bond 0.04891 ( 516) hydrogen bonds : angle 6.17781 ( 1407) link_ALPHA1-3 : bond 0.01116 ( 6) link_ALPHA1-3 : angle 2.22839 ( 18) link_ALPHA1-6 : bond 0.01149 ( 6) link_ALPHA1-6 : angle 1.92762 ( 18) link_BETA1-4 : bond 0.00484 ( 18) link_BETA1-4 : angle 1.51848 ( 54) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 2.64738 ( 12) *********************** 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 430 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 330 time to evaluate : 0.775 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: 0.7107 (t0) cc_final: 0.6691 (t0) REVERT: B 128 GLU cc_start: 0.4979 (tt0) cc_final: 0.4032 (tp30) REVERT: B 133 MET cc_start: 0.5085 (tpt) cc_final: 0.4593 (tpt) REVERT: C 79 PHE cc_start: 0.7932 (m-10) cc_final: 0.6928 (m-80) REVERT: C 104 ASP cc_start: 0.8839 (t0) cc_final: 0.8301 (t70) REVERT: C 172 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6802 (mp0) REVERT: C 174 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.5074 (p90) REVERT: D 37 ASP cc_start: 0.8255 (t0) cc_final: 0.7884 (t70) REVERT: D 69 GLU cc_start: 0.7944 (tt0) cc_final: 0.7542 (pt0) REVERT: D 123 LYS cc_start: 0.7712 (tttp) cc_final: 0.7484 (tttm) REVERT: D 128 GLU cc_start: 0.6210 (tm-30) cc_final: 0.4993 (tt0) REVERT: D 137 CYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5702 (m) REVERT: G 311 HIS cc_start: 0.7916 (m90) cc_final: 0.7502 (m90) REVERT: G 320 MET cc_start: 0.8604 (ppp) cc_final: 0.6970 (ppp) REVERT: I 69 GLU cc_start: 0.7842 (tt0) cc_final: 0.7430 (pt0) REVERT: I 90 ASP cc_start: 0.8468 (m-30) cc_final: 0.7928 (m-30) REVERT: E 43 GLN cc_start: 0.5750 (mt0) cc_final: 0.5115 (mt0) REVERT: E 55 ASP cc_start: 0.7754 (t0) cc_final: 0.7342 (t0) REVERT: E 69 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.6688 (tpp-160) REVERT: E 81 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5091 (mtp) REVERT: E 103 SER cc_start: 0.7735 (m) cc_final: 0.7494 (p) REVERT: J 18 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7014 (ttm110) REVERT: J 24 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7441 (mtp85) REVERT: K 18 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6859 (ttm110) REVERT: K 30 SER cc_start: 0.8021 (t) cc_final: 0.7163 (m) REVERT: K 31 ASN cc_start: 0.8207 (m-40) cc_final: 0.7994 (t0) REVERT: K 63 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7013 (m) REVERT: H 103 SER cc_start: 0.7810 (m) cc_final: 0.7422 (p) REVERT: L 24 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7035 (mtp85) REVERT: L 31 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7796 (t0) outliers start: 100 outliers final: 73 residues processed: 390 average time/residue: 0.1404 time to fit residues: 83.2068 Evaluate side-chains 384 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 LEU 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 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 267 ILE 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 D residue 167 LEU Chi-restraints excluded: chain G residue 102 VAL 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 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 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 20 LEU 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 4 MET 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 72 VAL Chi-restraints excluded: chain F residue 115 THR 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 70 ASP 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 H residue 117 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 70 ASP 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 143 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** 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** F 39 GLN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.134423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.118343 restraints weight = 41427.855| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.79 r_work: 0.3851 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17912 Z= 0.234 Angle : 0.769 10.958 24320 Z= 0.395 Chirality : 0.048 0.300 2757 Planarity : 0.005 0.054 3065 Dihedral : 9.276 74.610 3228 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.12 % Favored : 90.84 % Rotamer: Outliers : 5.75 % Allowed : 20.13 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.17), residues: 2139 helix: -0.18 (0.27), residues: 333 sheet: -1.35 (0.20), residues: 591 loop : -2.16 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.018 0.002 TYR G 98 PHE 0.060 0.002 PHE A 147 TRP 0.037 0.003 TRP H 36 HIS 0.010 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00525 (17857) covalent geometry : angle 0.75648 (24176) SS BOND : bond 0.00712 ( 21) SS BOND : angle 2.14931 ( 42) hydrogen bonds : bond 0.04812 ( 516) hydrogen bonds : angle 6.18700 ( 1407) link_ALPHA1-3 : bond 0.01027 ( 6) link_ALPHA1-3 : angle 2.16020 ( 18) link_ALPHA1-6 : bond 0.01181 ( 6) link_ALPHA1-6 : angle 1.93091 ( 18) link_BETA1-4 : bond 0.00456 ( 18) link_BETA1-4 : angle 1.48795 ( 54) link_NAG-ASN : bond 0.00425 ( 4) link_NAG-ASN : angle 2.54677 ( 12) *********************** 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 431 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 323 time to evaluate : 0.733 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: A 22 ASN cc_start: 0.7138 (t0) cc_final: 0.6754 (t0) REVERT: A 50 GLU cc_start: 0.7958 (tp30) cc_final: 0.7653 (tp30) REVERT: A 150 ARG cc_start: 0.7005 (mmp80) cc_final: 0.6321 (mmp80) REVERT: A 225 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 128 GLU cc_start: 0.5169 (tt0) cc_final: 0.4247 (tp30) REVERT: B 133 MET cc_start: 0.5115 (tpt) cc_final: 0.4659 (tpt) REVERT: C 79 PHE cc_start: 0.7914 (m-10) cc_final: 0.6983 (m-80) REVERT: C 104 ASP cc_start: 0.8757 (t0) cc_final: 0.8209 (t0) REVERT: C 119 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: C 172 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6659 (mp0) REVERT: C 174 PHE cc_start: 0.5294 (OUTLIER) cc_final: 0.5071 (p90) REVERT: D 37 ASP cc_start: 0.8299 (t0) cc_final: 0.7893 (t70) REVERT: D 69 GLU cc_start: 0.7882 (tt0) cc_final: 0.7509 (pt0) REVERT: D 122 THR cc_start: 0.8213 (m) cc_final: 0.7917 (m) REVERT: D 123 LYS cc_start: 0.7775 (tttp) cc_final: 0.7500 (tttm) REVERT: D 128 GLU cc_start: 0.6389 (tm-30) cc_final: 0.5130 (tt0) REVERT: D 137 CYS cc_start: 0.6705 (OUTLIER) cc_final: 0.5732 (p) REVERT: G 17 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7242 (m170) REVERT: G 85 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7615 (t0) REVERT: G 311 HIS cc_start: 0.7948 (m90) cc_final: 0.7551 (m90) REVERT: G 320 MET cc_start: 0.8634 (ppp) cc_final: 0.7028 (ppp) REVERT: I 17 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5320 (mmp) REVERT: I 69 GLU cc_start: 0.7894 (tt0) cc_final: 0.7430 (pt0) REVERT: I 90 ASP cc_start: 0.8431 (m-30) cc_final: 0.7903 (m-30) REVERT: E 43 GLN cc_start: 0.5816 (mt0) cc_final: 0.5561 (mt0) REVERT: E 55 ASP cc_start: 0.7830 (t0) cc_final: 0.7533 (t0) REVERT: E 69 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6708 (tpp-160) REVERT: E 70 LEU cc_start: 0.6907 (mt) cc_final: 0.6488 (tt) REVERT: E 81 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5427 (mtp) REVERT: E 103 SER cc_start: 0.7727 (m) cc_final: 0.7482 (p) REVERT: J 24 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7454 (mtp85) REVERT: J 30 SER cc_start: 0.7988 (t) cc_final: 0.7305 (m) REVERT: J 46 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5993 (mp) REVERT: J 48 ILE cc_start: 0.5491 (mm) cc_final: 0.5200 (mm) REVERT: K 18 ARG cc_start: 0.7053 (ttt90) cc_final: 0.6808 (ttm110) REVERT: K 30 SER cc_start: 0.8081 (t) cc_final: 0.7186 (m) REVERT: K 31 ASN cc_start: 0.8184 (m-40) cc_final: 0.7979 (t0) REVERT: K 44 ILE cc_start: 0.5845 (mt) cc_final: 0.5419 (mt) REVERT: K 63 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7103 (m) REVERT: H 20 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8121 (tp) REVERT: H 57 TYR cc_start: 0.4415 (t80) cc_final: 0.4065 (t80) REVERT: H 103 SER cc_start: 0.7739 (m) cc_final: 0.7357 (p) REVERT: L 31 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7874 (t0) outliers start: 108 outliers final: 79 residues processed: 393 average time/residue: 0.1366 time to fit residues: 82.3004 Evaluate side-chains 391 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 300 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 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 167 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 175 ASP 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 267 ILE 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 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 102 VAL 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 151 SER 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 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 4 MET 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 12 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 51 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 K residue 96 ARG Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 91 SER 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 85 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 63 optimal weight: 0.0030 chunk 204 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** 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 ** 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.136216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.120182 restraints weight = 41003.182| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.79 r_work: 0.3878 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17912 Z= 0.176 Angle : 0.729 10.440 24320 Z= 0.374 Chirality : 0.046 0.283 2757 Planarity : 0.004 0.053 3065 Dihedral : 8.806 70.179 3228 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.74 % Favored : 91.21 % Rotamer: Outliers : 4.53 % Allowed : 22.10 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.17), residues: 2139 helix: -0.13 (0.27), residues: 336 sheet: -1.41 (0.20), residues: 615 loop : -2.08 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 40 TYR 0.015 0.002 TYR C 98 PHE 0.035 0.002 PHE A 147 TRP 0.060 0.003 TRP L 35 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00393 (17857) covalent geometry : angle 0.71813 (24176) SS BOND : bond 0.00535 ( 21) SS BOND : angle 1.86616 ( 42) hydrogen bonds : bond 0.04544 ( 516) hydrogen bonds : angle 6.13707 ( 1407) link_ALPHA1-3 : bond 0.01100 ( 6) link_ALPHA1-3 : angle 2.09203 ( 18) link_ALPHA1-6 : bond 0.01037 ( 6) link_ALPHA1-6 : angle 1.89471 ( 18) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.40639 ( 54) link_NAG-ASN : bond 0.00385 ( 4) link_NAG-ASN : angle 2.28098 ( 12) *********************** 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 422 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 337 time to evaluate : 0.747 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: 0.7078 (t0) cc_final: 0.6724 (t0) REVERT: A 50 GLU cc_start: 0.7914 (tp30) cc_final: 0.7547 (tp30) REVERT: A 120 PHE cc_start: 0.7621 (t80) cc_final: 0.7394 (t80) REVERT: A 150 ARG cc_start: 0.6900 (mmp80) cc_final: 0.6283 (mmp80) REVERT: A 225 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7108 (t0) REVERT: B 46 ASP cc_start: 0.8179 (m-30) cc_final: 0.7909 (m-30) REVERT: B 128 GLU cc_start: 0.5141 (tt0) cc_final: 0.4222 (tp30) REVERT: B 133 MET cc_start: 0.5057 (tpt) cc_final: 0.4631 (tpt) REVERT: C 79 PHE cc_start: 0.7876 (m-10) cc_final: 0.7017 (m-80) REVERT: C 104 ASP cc_start: 0.8698 (t0) cc_final: 0.8141 (t0) REVERT: C 119 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: C 172 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6814 (mp0) REVERT: C 320 MET cc_start: 0.8582 (ppp) cc_final: 0.8185 (ppp) REVERT: D 37 ASP cc_start: 0.8206 (t0) cc_final: 0.7815 (t70) REVERT: D 69 GLU cc_start: 0.7870 (tt0) cc_final: 0.7399 (pt0) REVERT: D 122 THR cc_start: 0.8160 (m) cc_final: 0.7879 (m) REVERT: D 123 LYS cc_start: 0.7635 (tttp) cc_final: 0.7324 (tttm) REVERT: D 128 GLU cc_start: 0.6326 (tm-30) cc_final: 0.5181 (tt0) REVERT: D 137 CYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6878 (m) REVERT: G 15 LEU cc_start: 0.7549 (tt) cc_final: 0.7345 (tp) REVERT: G 17 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6993 (m170) REVERT: G 311 HIS cc_start: 0.7859 (m90) cc_final: 0.7416 (m90) REVERT: G 320 MET cc_start: 0.8648 (ppp) cc_final: 0.7263 (ppp) REVERT: I 69 GLU cc_start: 0.7907 (tt0) cc_final: 0.7475 (pt0) REVERT: I 90 ASP cc_start: 0.8431 (m-30) cc_final: 0.7907 (m-30) REVERT: E 43 GLN cc_start: 0.5820 (mt0) cc_final: 0.5527 (mt0) REVERT: E 55 ASP cc_start: 0.7813 (t0) cc_final: 0.7509 (t0) REVERT: E 69 ARG cc_start: 0.7095 (tpp-160) cc_final: 0.6647 (tpp-160) REVERT: E 70 LEU cc_start: 0.6987 (mt) cc_final: 0.6447 (tt) REVERT: E 81 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5502 (mtp) REVERT: E 103 SER cc_start: 0.7645 (m) cc_final: 0.7393 (p) REVERT: J 3 GLN cc_start: 0.6132 (pp30) cc_final: 0.5136 (mp10) REVERT: J 4 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6784 (ttt) REVERT: J 24 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7423 (mtp85) REVERT: J 30 SER cc_start: 0.7971 (t) cc_final: 0.7327 (m) REVERT: J 44 ILE cc_start: 0.5387 (mt) cc_final: 0.5037 (mt) REVERT: J 46 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5818 (mp) REVERT: J 48 ILE cc_start: 0.5080 (mm) cc_final: 0.4864 (mm) REVERT: J 63 SER cc_start: 0.7969 (t) cc_final: 0.7420 (m) REVERT: K 18 ARG cc_start: 0.7056 (ttt90) cc_final: 0.6788 (ttm110) REVERT: K 30 SER cc_start: 0.8072 (t) cc_final: 0.7253 (m) REVERT: K 31 ASN cc_start: 0.8152 (m-40) cc_final: 0.7944 (t0) REVERT: H 103 SER cc_start: 0.7645 (m) cc_final: 0.7255 (p) REVERT: L 31 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7727 (t0) REVERT: L 35 TRP cc_start: 0.6911 (m-10) cc_final: 0.6524 (m-10) outliers start: 85 outliers final: 66 residues processed: 389 average time/residue: 0.1382 time to fit residues: 82.3170 Evaluate side-chains 385 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 146 ASN Chi-restraints excluded: chain C residue 17 HIS 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 167 THR Chi-restraints excluded: chain C residue 175 ASP 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 D residue 38 LEU 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 102 VAL 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 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 28 ASN Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 116 ASN 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 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 89 GLN 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 114 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 296 ASN ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 75 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 60 ASN ** 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.136759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120711 restraints weight = 41143.614| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.79 r_work: 0.3887 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17912 Z= 0.161 Angle : 0.716 9.450 24320 Z= 0.369 Chirality : 0.046 0.273 2757 Planarity : 0.004 0.053 3065 Dihedral : 8.429 65.682 3228 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 4.53 % Allowed : 22.79 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.17), residues: 2139 helix: -0.04 (0.27), residues: 336 sheet: -1.38 (0.21), residues: 615 loop : -2.02 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 40 TYR 0.018 0.002 TYR J 86 PHE 0.032 0.002 PHE A 147 TRP 0.094 0.003 TRP H 36 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00357 (17857) covalent geometry : angle 0.70511 (24176) SS BOND : bond 0.00512 ( 21) SS BOND : angle 1.84869 ( 42) hydrogen bonds : bond 0.04276 ( 516) hydrogen bonds : angle 6.02435 ( 1407) link_ALPHA1-3 : bond 0.01014 ( 6) link_ALPHA1-3 : angle 2.03654 ( 18) link_ALPHA1-6 : bond 0.00976 ( 6) link_ALPHA1-6 : angle 1.83945 ( 18) link_BETA1-4 : bond 0.00392 ( 18) link_BETA1-4 : angle 1.35750 ( 54) link_NAG-ASN : bond 0.00388 ( 4) link_NAG-ASN : angle 2.17723 ( 12) *********************** 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 414 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 329 time to evaluate : 0.765 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: 0.7024 (t0) cc_final: 0.6684 (t0) REVERT: A 150 ARG cc_start: 0.6855 (mmp80) cc_final: 0.6290 (mmp80) REVERT: A 225 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7109 (t0) REVERT: A 261 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7807 (ptp-110) REVERT: B 128 GLU cc_start: 0.5029 (tt0) cc_final: 0.4301 (tp30) REVERT: B 133 MET cc_start: 0.5079 (tpt) cc_final: 0.4696 (tpt) REVERT: C 79 PHE cc_start: 0.7861 (m-10) cc_final: 0.7068 (m-80) REVERT: C 104 ASP cc_start: 0.8677 (t0) cc_final: 0.8083 (t70) REVERT: C 119 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: C 172 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6655 (mp0) REVERT: C 320 MET cc_start: 0.8597 (ppp) cc_final: 0.8235 (ppp) REVERT: D 32 ARG cc_start: 0.7114 (ptp-170) cc_final: 0.6421 (ptp-170) REVERT: D 37 ASP cc_start: 0.8150 (t0) cc_final: 0.7763 (t70) REVERT: D 69 GLU cc_start: 0.7826 (tt0) cc_final: 0.7366 (pt0) REVERT: D 122 THR cc_start: 0.8138 (m) cc_final: 0.7847 (m) REVERT: D 123 LYS cc_start: 0.7617 (tttp) cc_final: 0.7303 (tttm) REVERT: D 128 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5105 (tt0) REVERT: D 141 TYR cc_start: 0.5914 (t80) cc_final: 0.5585 (t80) REVERT: G 17 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6879 (m170) REVERT: G 104 ASP cc_start: 0.8519 (t0) cc_final: 0.8023 (t70) REVERT: G 311 HIS cc_start: 0.7827 (m90) cc_final: 0.7405 (m90) REVERT: G 320 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7217 (ppp) REVERT: I 69 GLU cc_start: 0.7885 (tt0) cc_final: 0.7490 (pt0) REVERT: I 90 ASP cc_start: 0.8398 (m-30) cc_final: 0.7973 (m-30) REVERT: E 43 GLN cc_start: 0.5895 (mt0) cc_final: 0.5574 (mt0) REVERT: E 55 ASP cc_start: 0.7818 (t0) cc_final: 0.7514 (t0) REVERT: E 69 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6630 (tpp-160) REVERT: E 70 LEU cc_start: 0.6978 (mt) cc_final: 0.6433 (tt) REVERT: E 81 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5554 (mtp) REVERT: E 103 SER cc_start: 0.7622 (m) cc_final: 0.7376 (p) REVERT: J 3 GLN cc_start: 0.6044 (pp30) cc_final: 0.5133 (mp10) REVERT: J 4 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6791 (ttt) REVERT: J 24 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7391 (mtp85) REVERT: J 30 SER cc_start: 0.7986 (t) cc_final: 0.7361 (m) REVERT: J 46 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5982 (mp) REVERT: K 18 ARG cc_start: 0.7089 (ttt90) cc_final: 0.6805 (ttm110) REVERT: K 30 SER cc_start: 0.8069 (t) cc_final: 0.7247 (m) REVERT: K 31 ASN cc_start: 0.8160 (m-40) cc_final: 0.7901 (t0) REVERT: K 103 LYS cc_start: 0.7065 (tttt) cc_final: 0.6693 (pttp) REVERT: H 28 THR cc_start: 0.7710 (m) cc_final: 0.7163 (p) REVERT: H 69 ARG cc_start: 0.7295 (ttp-170) cc_final: 0.6910 (ttp-170) REVERT: H 103 SER cc_start: 0.7653 (m) cc_final: 0.7444 (t) REVERT: L 18 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6977 (ttm110) REVERT: L 24 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7921 (mtp85) REVERT: L 31 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7850 (t0) outliers start: 85 outliers final: 69 residues processed: 383 average time/residue: 0.1385 time to fit residues: 80.8807 Evaluate side-chains 385 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 20 VAL 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 197 GLN 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 146 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 96 ASN 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 167 THR 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 267 ILE Chi-restraints excluded: chain C residue 300 ILE 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 102 VAL 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 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 G residue 320 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 38 LEU 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 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 89 GLN 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 121 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 145 optimal weight: 0.0370 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 103 optimal weight: 0.0270 overall best weight: 1.1718 ------------------------------------------------------------------------------- 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 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 62 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.137363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.121326 restraints weight = 40795.761| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.78 r_work: 0.3891 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17912 Z= 0.153 Angle : 0.724 12.415 24320 Z= 0.371 Chirality : 0.046 0.264 2757 Planarity : 0.004 0.053 3065 Dihedral : 8.178 61.476 3228 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.27 % Favored : 91.68 % Rotamer: Outliers : 4.15 % Allowed : 23.22 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.17), residues: 2139 helix: 0.01 (0.27), residues: 336 sheet: -1.38 (0.21), residues: 621 loop : -2.00 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.017 0.002 TYR C 195 PHE 0.029 0.002 PHE A 147 TRP 0.095 0.003 TRP L 35 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00340 (17857) covalent geometry : angle 0.71448 (24176) SS BOND : bond 0.00625 ( 21) SS BOND : angle 1.86356 ( 42) hydrogen bonds : bond 0.04192 ( 516) hydrogen bonds : angle 6.00168 ( 1407) link_ALPHA1-3 : bond 0.00997 ( 6) link_ALPHA1-3 : angle 2.00559 ( 18) link_ALPHA1-6 : bond 0.00960 ( 6) link_ALPHA1-6 : angle 1.80341 ( 18) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.32100 ( 54) link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 2.05762 ( 12) ********************** 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 399 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7123 (t0) cc_final: 0.6771 (t0) REVERT: A 57 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5858 (tm-30) REVERT: A 120 PHE cc_start: 0.7636 (t80) cc_final: 0.7350 (t80) REVERT: A 150 ARG cc_start: 0.6742 (mmp80) cc_final: 0.6356 (mmp80) REVERT: A 225 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7090 (t0) REVERT: A 261 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7822 (ptp-110) REVERT: B 133 MET cc_start: 0.5008 (tpt) cc_final: 0.4653 (tpt) REVERT: C 79 PHE cc_start: 0.7833 (m-10) cc_final: 0.6978 (m-80) REVERT: C 104 ASP cc_start: 0.8660 (t0) cc_final: 0.8075 (t70) REVERT: C 119 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 172 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6751 (mp0) REVERT: C 225 ASP cc_start: 0.7132 (t0) cc_final: 0.6893 (t0) REVERT: C 280 GLU cc_start: 0.6932 (pm20) cc_final: 0.6707 (pm20) REVERT: C 320 MET cc_start: 0.8580 (ppp) cc_final: 0.8219 (ppp) REVERT: D 32 ARG cc_start: 0.7158 (ptp-170) cc_final: 0.6397 (ptp-170) REVERT: D 37 ASP cc_start: 0.8123 (t0) cc_final: 0.7736 (t70) REVERT: D 69 GLU cc_start: 0.7845 (tt0) cc_final: 0.7364 (pt0) REVERT: D 122 THR cc_start: 0.8145 (m) cc_final: 0.7855 (m) REVERT: D 123 LYS cc_start: 0.7620 (tttp) cc_final: 0.7335 (tttm) REVERT: D 128 GLU cc_start: 0.6238 (tm-30) cc_final: 0.5095 (tt0) REVERT: D 141 TYR cc_start: 0.5900 (t80) cc_final: 0.5612 (t80) REVERT: G 17 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6776 (m170) REVERT: G 104 ASP cc_start: 0.8508 (t0) cc_final: 0.8008 (t70) REVERT: G 311 HIS cc_start: 0.7751 (m90) cc_final: 0.7374 (m90) REVERT: G 320 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7140 (ppp) REVERT: I 17 MET cc_start: 0.6156 (mmp) cc_final: 0.5236 (mmt) REVERT: I 69 GLU cc_start: 0.7899 (tt0) cc_final: 0.7530 (pt0) REVERT: I 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.7964 (m-30) REVERT: E 43 GLN cc_start: 0.5839 (mt0) cc_final: 0.5487 (mt0) REVERT: E 55 ASP cc_start: 0.7857 (t0) cc_final: 0.7549 (t0) REVERT: E 69 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6669 (tpp-160) REVERT: E 70 LEU cc_start: 0.6979 (mt) cc_final: 0.6250 (tt) REVERT: E 81 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5536 (mtp) REVERT: E 103 SER cc_start: 0.7617 (m) cc_final: 0.7368 (p) REVERT: J 3 GLN cc_start: 0.5977 (pp30) cc_final: 0.5075 (mp10) REVERT: J 4 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6796 (ttt) REVERT: J 24 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7336 (mtp85) REVERT: J 30 SER cc_start: 0.7972 (t) cc_final: 0.7352 (m) REVERT: J 34 ASN cc_start: 0.7711 (m-40) cc_final: 0.7477 (m110) REVERT: J 46 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6042 (mp) REVERT: K 18 ARG cc_start: 0.7071 (ttt90) cc_final: 0.6811 (ttm110) REVERT: K 30 SER cc_start: 0.8055 (t) cc_final: 0.7214 (m) REVERT: K 31 ASN cc_start: 0.8144 (m-40) cc_final: 0.7886 (t0) REVERT: K 63 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.7026 (m) REVERT: K 103 LYS cc_start: 0.7097 (tttt) cc_final: 0.6709 (pttp) REVERT: H 55 ASP cc_start: 0.8167 (t0) cc_final: 0.7941 (t0) REVERT: H 69 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.6916 (ttp-170) REVERT: H 81 MET cc_start: 0.5938 (mtp) cc_final: 0.5728 (ttm) REVERT: L 31 ASN cc_start: 0.8200 (t0) cc_final: 0.7824 (t0) outliers start: 78 outliers final: 65 residues processed: 371 average time/residue: 0.1299 time to fit residues: 72.8479 Evaluate side-chains 382 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 57 GLN 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 197 GLN 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 146 ASN Chi-restraints excluded: chain C residue 96 ASN 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 167 THR 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 206 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 172 GLU 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 G residue 320 MET Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 38 LEU 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 81 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain J residue 4 MET 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 75 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN 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 116 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 34 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 295 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.137057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.121095 restraints weight = 41019.203| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.79 r_work: 0.3888 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17912 Z= 0.157 Angle : 0.725 11.574 24320 Z= 0.370 Chirality : 0.046 0.259 2757 Planarity : 0.004 0.054 3065 Dihedral : 7.940 59.323 3228 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.27 % Favored : 91.68 % Rotamer: Outliers : 3.73 % Allowed : 24.17 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.17), residues: 2139 helix: -0.03 (0.27), residues: 336 sheet: -1.45 (0.20), residues: 627 loop : -2.00 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 40 TYR 0.017 0.002 TYR J 86 PHE 0.027 0.002 PHE A 147 TRP 0.081 0.003 TRP L 35 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00350 (17857) covalent geometry : angle 0.71450 (24176) SS BOND : bond 0.00603 ( 21) SS BOND : angle 2.06763 ( 42) hydrogen bonds : bond 0.04227 ( 516) hydrogen bonds : angle 5.95408 ( 1407) link_ALPHA1-3 : bond 0.00982 ( 6) link_ALPHA1-3 : angle 1.98671 ( 18) link_ALPHA1-6 : bond 0.00975 ( 6) link_ALPHA1-6 : angle 1.79125 ( 18) link_BETA1-4 : bond 0.00405 ( 18) link_BETA1-4 : angle 1.30152 ( 54) link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 2.01432 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4344.45 seconds wall clock time: 76 minutes 0.52 seconds (4560.52 seconds total)