Starting phenix.real_space_refine on Mon Nov 18 20:25:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_41705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_41705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_41705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_41705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txu_41705/11_2024/8txu_41705.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10909 2.51 5 N 2963 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17503 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "B" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "C" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "G" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.04, per 1000 atoms: 0.63 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: 5.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3978 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 47 sheets defined 16.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.596A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 80' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.186A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 111 Processing helix chain 'B' and resid 115 through 124 removed outlier: 4.174A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.919A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 111 Processing helix chain 'D' and resid 114 through 127 removed outlier: 4.593A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 65 through 71 Processing helix chain 'G' and resid 104 through 116 Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 37 through 54 removed outlier: 4.035A pdb=" N ARG I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 111 removed outlier: 3.614A pdb=" N ASP I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 127 removed outlier: 4.610A pdb=" N LYS I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN I 125 " --> pdb=" O LYS I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.652A pdb=" N ILE I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.635A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.554A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE J 83 " --> pdb=" O GLN J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.963A pdb=" N LYS F 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.735A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.606A pdb=" N ASP K 82 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE K 83 " --> pdb=" O GLN K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.611A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.759A pdb=" N PHE B 138 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.607A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.621A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.658A pdb=" N THR A 155 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 7.145A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.935A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.577A pdb=" N GLY A 303 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 28 removed outlier: 3.532A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN B 28 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.510A pdb=" N THR C 40 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.437A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.741A pdb=" N ARG C 90 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.599A pdb=" N LEU C 154 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 251 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.934A pdb=" N LEU C 243 " --> pdb=" O MET C 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 179 through 184 Processing sheet with id=AC4, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.666A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 52 removed outlier: 6.619A pdb=" N ILE G 51 " --> pdb=" O GLY G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 3.620A pdb=" N VAL G 88 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AD2, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.943A pdb=" N LEU G 243 " --> pdb=" O MET G 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 179 through 184 Processing sheet with id=AD4, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.716A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 81 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.667A pdb=" N GLU E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.818A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AE1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.477A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.637A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.567A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.812A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.758A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.669A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.669A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 5.83 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: 4.610 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 42.230 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.360 ------------------------------------------------------------------------------- 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 17857 Z= 0.338 Angle : 0.937 10.411 24176 Z= 0.489 Chirality : 0.056 0.370 2757 Planarity : 0.006 0.113 3065 Dihedral : 17.719 110.461 7227 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 0.37 % Allowed : 0.75 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 2139 helix: -0.17 (0.27), residues: 297 sheet: -0.92 (0.22), residues: 609 loop : -1.95 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 14 HIS 0.013 0.002 HIS G 18 PHE 0.034 0.002 PHE I 9 TYR 0.027 0.002 TYR B 141 ARG 0.010 0.001 ARG A 229 *********************** 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 : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6191 (t0) cc_final: 0.5981 (t0) REVERT: A 169 PRO cc_start: 0.7381 (Cg_endo) cc_final: 0.7059 (Cg_exo) REVERT: A 173 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 262 SER cc_start: 0.8640 (m) cc_final: 0.8358 (p) REVERT: B 22 TYR cc_start: 0.7106 (m-10) cc_final: 0.6847 (m-80) REVERT: B 67 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6729 (tt0) REVERT: C 79 PHE cc_start: 0.7184 (m-10) cc_final: 0.6502 (m-10) REVERT: C 276 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7194 (mmmt) REVERT: D 67 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6787 (tt0) REVERT: D 69 GLU cc_start: 0.7630 (tt0) cc_final: 0.6962 (pt0) REVERT: D 128 GLU cc_start: 0.5692 (tm-30) cc_final: 0.4751 (tt0) REVERT: D 133 MET cc_start: 0.3306 (tmm) cc_final: 0.2623 (tpt) REVERT: G 188 ASP cc_start: 0.6199 (t0) cc_final: 0.5804 (p0) REVERT: G 262 SER cc_start: 0.8589 (t) cc_final: 0.8378 (p) REVERT: G 276 LYS cc_start: 0.7386 (mmtm) cc_final: 0.7152 (mmmt) REVERT: I 67 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6835 (tt0) REVERT: I 69 GLU cc_start: 0.7197 (tt0) cc_final: 0.6959 (pt0) REVERT: I 93 SER cc_start: 0.8734 (p) cc_final: 0.8529 (t) REVERT: E 43 GLN cc_start: 0.6334 (mt0) cc_final: 0.5891 (mt0) REVERT: E 103 SER cc_start: 0.6794 (m) cc_final: 0.6575 (p) REVERT: J 3 GLN cc_start: 0.6539 (pp30) cc_final: 0.5985 (mp10) REVERT: J 51 THR cc_start: 0.6694 (t) cc_final: 0.6128 (t) REVERT: J 74 THR cc_start: 0.7637 (m) cc_final: 0.7432 (m) REVERT: K 18 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7123 (ttm170) REVERT: H 28 THR cc_start: 0.7499 (m) cc_final: 0.6891 (p) REVERT: H 32 TYR cc_start: 0.7672 (m-80) cc_final: 0.7430 (m-80) REVERT: H 103 SER cc_start: 0.7101 (m) cc_final: 0.6783 (p) REVERT: L 29 ILE cc_start: 0.6861 (pt) cc_final: 0.6438 (pt) outliers start: 7 outliers final: 0 residues processed: 603 average time/residue: 0.3050 time to fit residues: 272.8726 Evaluate side-chains 364 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 129 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN G 158 ASN G 191 GLN G 250 ASN I 42 GLN ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 77 ASN J 89 GLN F 5 GLN K 77 ASN L 3 GLN L 77 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17857 Z= 0.210 Angle : 0.675 7.524 24176 Z= 0.354 Chirality : 0.046 0.273 2757 Planarity : 0.005 0.075 3065 Dihedral : 13.796 91.276 3228 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.88 % Allowed : 13.84 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2139 helix: 0.36 (0.28), residues: 321 sheet: -0.94 (0.21), residues: 636 loop : -1.77 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 36 HIS 0.008 0.001 HIS G 18 PHE 0.016 0.002 PHE I 63 TYR 0.032 0.002 TYR H 101 ARG 0.005 0.001 ARG A 201 *********************** 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 453 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 2.150 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: 0.6201 (t0) cc_final: 0.5936 (t0) REVERT: A 191 GLN cc_start: 0.5449 (tt0) cc_final: 0.5077 (tt0) REVERT: A 262 SER cc_start: 0.8626 (m) cc_final: 0.8322 (p) REVERT: B 67 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6663 (tt0) REVERT: B 128 GLU cc_start: 0.4476 (tt0) cc_final: 0.3229 (tp30) REVERT: B 133 MET cc_start: 0.4009 (tpt) cc_final: 0.3759 (tpt) REVERT: C 79 PHE cc_start: 0.7289 (m-10) cc_final: 0.6545 (m-10) REVERT: C 276 LYS cc_start: 0.7513 (mmtm) cc_final: 0.7300 (mmmt) REVERT: D 69 GLU cc_start: 0.7615 (tt0) cc_final: 0.7318 (pt0) REVERT: D 123 LYS cc_start: 0.7657 (tptt) cc_final: 0.7324 (pptt) REVERT: D 128 GLU cc_start: 0.5510 (tm-30) cc_final: 0.4636 (tt0) REVERT: D 133 MET cc_start: 0.3573 (tmm) cc_final: 0.2826 (tpt) REVERT: G 188 ASP cc_start: 0.6320 (t0) cc_final: 0.5859 (p0) REVERT: I 42 GLN cc_start: 0.8417 (tp40) cc_final: 0.8217 (tp-100) REVERT: I 67 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6874 (tt0) REVERT: I 69 GLU cc_start: 0.7297 (tt0) cc_final: 0.7003 (pt0) REVERT: I 90 ASP cc_start: 0.7951 (m-30) cc_final: 0.7543 (m-30) REVERT: E 43 GLN cc_start: 0.6313 (mt0) cc_final: 0.5910 (mt0) REVERT: E 55 ASP cc_start: 0.7130 (t0) cc_final: 0.6885 (t0) REVERT: J 3 GLN cc_start: 0.6091 (pp30) cc_final: 0.5801 (mp10) REVERT: J 4 MET cc_start: 0.7077 (ttm) cc_final: 0.6796 (ttt) REVERT: J 18 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7015 (ttm170) REVERT: F 69 ARG cc_start: 0.6327 (ptp-170) cc_final: 0.6019 (ptp-170) REVERT: F 80 TYR cc_start: 0.5712 (m-80) cc_final: 0.5508 (m-80) REVERT: H 28 THR cc_start: 0.7592 (m) cc_final: 0.7031 (p) REVERT: H 32 TYR cc_start: 0.7899 (m-80) cc_final: 0.7683 (m-80) REVERT: H 36 TRP cc_start: 0.6879 (m100) cc_final: 0.6665 (m100) REVERT: H 81 MET cc_start: 0.3967 (OUTLIER) cc_final: 0.3680 (mtp) REVERT: H 103 SER cc_start: 0.7260 (m) cc_final: 0.6895 (p) REVERT: L 34 ASN cc_start: 0.7524 (m-40) cc_final: 0.6967 (m-40) outliers start: 54 outliers final: 36 residues processed: 428 average time/residue: 0.2950 time to fit residues: 191.2731 Evaluate side-chains 372 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 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 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 C residue 288 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 191 GLN Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 19 VAL 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 105 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN ** 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN K 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 17857 Z= 0.420 Angle : 0.820 10.598 24176 Z= 0.427 Chirality : 0.051 0.295 2757 Planarity : 0.006 0.068 3065 Dihedral : 12.081 91.247 3228 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 4.90 % Allowed : 16.03 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2139 helix: -0.04 (0.27), residues: 333 sheet: -0.89 (0.22), residues: 570 loop : -2.03 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 36 HIS 0.010 0.002 HIS G 18 PHE 0.021 0.002 PHE C 148 TYR 0.038 0.003 TYR C 195 ARG 0.010 0.001 ARG I 32 *********************** 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 445 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 1.933 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: 0.6737 (t0) cc_final: 0.6420 (t0) REVERT: A 75 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A 230 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7189 (tp) REVERT: A 245 ILE cc_start: 0.8701 (mm) cc_final: 0.8430 (mm) REVERT: B 128 GLU cc_start: 0.4557 (tt0) cc_final: 0.3461 (tp30) REVERT: B 133 MET cc_start: 0.4386 (tpt) cc_final: 0.3977 (tpt) REVERT: C 35 GLU cc_start: 0.6870 (tt0) cc_final: 0.6591 (tt0) REVERT: C 62 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6354 (mt-10) REVERT: C 79 PHE cc_start: 0.7561 (m-10) cc_final: 0.6760 (m-80) REVERT: D 37 ASP cc_start: 0.7983 (t0) cc_final: 0.7715 (t70) REVERT: D 69 GLU cc_start: 0.7706 (tt0) cc_final: 0.7294 (pt0) REVERT: D 128 GLU cc_start: 0.5838 (tm-30) cc_final: 0.4742 (tt0) REVERT: D 129 ASN cc_start: 0.3661 (OUTLIER) cc_final: 0.3458 (p0) REVERT: G 22 ASN cc_start: 0.7360 (m110) cc_final: 0.7016 (p0) REVERT: I 37 ASP cc_start: 0.6883 (t70) cc_final: 0.6369 (t70) REVERT: I 67 GLU cc_start: 0.7738 (mm-30) cc_final: 0.6935 (tt0) REVERT: I 69 GLU cc_start: 0.7611 (tt0) cc_final: 0.7276 (pt0) REVERT: I 90 ASP cc_start: 0.8030 (m-30) cc_final: 0.7646 (m-30) REVERT: E 36 TRP cc_start: 0.6798 (m100) cc_final: 0.6147 (m-10) REVERT: E 55 ASP cc_start: 0.7410 (t0) cc_final: 0.7115 (t0) REVERT: E 67 LYS cc_start: 0.6216 (tmtt) cc_final: 0.5594 (tptm) REVERT: E 81 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.3307 (mtp) REVERT: J 3 GLN cc_start: 0.6101 (pp30) cc_final: 0.5713 (mp10) REVERT: J 4 MET cc_start: 0.7225 (ttm) cc_final: 0.6903 (ttt) REVERT: J 18 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7095 (ttm110) REVERT: H 36 TRP cc_start: 0.6932 (m100) cc_final: 0.6634 (m100) REVERT: H 81 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4683 (mtp) REVERT: H 103 SER cc_start: 0.7712 (m) cc_final: 0.7408 (p) REVERT: L 54 LEU cc_start: 0.5924 (tp) cc_final: 0.5485 (pp) outliers start: 92 outliers final: 56 residues processed: 401 average time/residue: 0.3050 time to fit residues: 184.2569 Evaluate side-chains 362 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 151 LEU 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 230 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL 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 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 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 79 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 81 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 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 12 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain 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 76 SER 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 188 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 91 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 156 HIS C 197 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN E 6 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17857 Z= 0.189 Angle : 0.659 9.144 24176 Z= 0.340 Chirality : 0.046 0.312 2757 Planarity : 0.004 0.059 3065 Dihedral : 10.517 83.563 3228 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 3.25 % Allowed : 18.69 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2139 helix: 0.36 (0.27), residues: 333 sheet: -0.97 (0.22), residues: 585 loop : -1.82 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 36 HIS 0.008 0.001 HIS G 18 PHE 0.017 0.001 PHE C 148 TYR 0.015 0.002 TYR E 106 ARG 0.006 0.000 ARG H 40 *********************** 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 414 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 1.957 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: 0.6491 (t0) cc_final: 0.6115 (t0) REVERT: A 75 GLN cc_start: 0.7156 (tp40) cc_final: 0.6955 (tt0) REVERT: B 32 ARG cc_start: 0.5884 (ptm160) cc_final: 0.5128 (ptm160) REVERT: B 128 GLU cc_start: 0.4417 (tt0) cc_final: 0.3344 (tp30) REVERT: C 35 GLU cc_start: 0.6615 (tt0) cc_final: 0.6369 (tt0) REVERT: C 62 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6470 (mt-10) REVERT: C 79 PHE cc_start: 0.7389 (m-10) cc_final: 0.6557 (m-80) REVERT: C 320 MET cc_start: 0.8152 (ppp) cc_final: 0.7844 (ppp) REVERT: D 37 ASP cc_start: 0.7795 (t0) cc_final: 0.7494 (t70) REVERT: D 42 GLN cc_start: 0.8420 (tp40) cc_final: 0.7868 (tp-100) REVERT: D 69 GLU cc_start: 0.7562 (tt0) cc_final: 0.7214 (pt0) REVERT: D 128 GLU cc_start: 0.6114 (tm-30) cc_final: 0.5053 (tt0) REVERT: G 22 ASN cc_start: 0.7147 (m110) cc_final: 0.6869 (p0) REVERT: G 320 MET cc_start: 0.8224 (ppp) cc_final: 0.7995 (ppp) REVERT: I 37 ASP cc_start: 0.6743 (t70) cc_final: 0.6223 (t70) REVERT: I 90 ASP cc_start: 0.7948 (m-30) cc_final: 0.7554 (m-30) REVERT: E 55 ASP cc_start: 0.7436 (t0) cc_final: 0.7073 (t0) REVERT: J 18 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7111 (ttm110) REVERT: J 73 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6726 (mp) REVERT: K 30 SER cc_start: 0.7744 (t) cc_final: 0.6986 (m) REVERT: H 36 TRP cc_start: 0.6585 (m100) cc_final: 0.6382 (m100) REVERT: H 81 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4936 (mtp) REVERT: H 103 SER cc_start: 0.7540 (m) cc_final: 0.7223 (p) REVERT: L 18 ARG cc_start: 0.7529 (ttt-90) cc_final: 0.7102 (ttm170) REVERT: L 54 LEU cc_start: 0.6207 (tp) cc_final: 0.6003 (pp) outliers start: 61 outliers final: 32 residues processed: 391 average time/residue: 0.2860 time to fit residues: 170.9546 Evaluate side-chains 353 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** 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 22 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 17857 Z= 0.450 Angle : 0.824 11.813 24176 Z= 0.429 Chirality : 0.050 0.324 2757 Planarity : 0.005 0.058 3065 Dihedral : 10.179 84.421 3228 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.29 % Favored : 89.67 % Rotamer: Outliers : 5.48 % Allowed : 18.21 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 2139 helix: 0.04 (0.28), residues: 327 sheet: -1.25 (0.21), residues: 606 loop : -2.03 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 36 HIS 0.011 0.002 HIS C 18 PHE 0.020 0.002 PHE C 148 TYR 0.028 0.003 TYR G 98 ARG 0.004 0.001 ARG H 40 *********************** 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 425 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 322 time to evaluate : 1.938 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: 0.6965 (t0) cc_final: 0.6552 (t0) REVERT: B 128 GLU cc_start: 0.4613 (tt0) cc_final: 0.3658 (tp30) REVERT: C 17 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.5933 (m90) REVERT: C 62 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6355 (mt-10) REVERT: C 79 PHE cc_start: 0.7738 (m-10) cc_final: 0.6881 (m-80) REVERT: D 37 ASP cc_start: 0.8124 (t0) cc_final: 0.7684 (t70) REVERT: D 69 GLU cc_start: 0.7686 (tt0) cc_final: 0.7343 (pt0) REVERT: D 128 GLU cc_start: 0.5947 (tm-30) cc_final: 0.4905 (tt0) REVERT: I 90 ASP cc_start: 0.8112 (m-30) cc_final: 0.7910 (m-30) REVERT: E 55 ASP cc_start: 0.7384 (t0) cc_final: 0.6948 (t0) REVERT: J 18 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7205 (ttm110) REVERT: J 46 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6273 (mp) REVERT: H 103 SER cc_start: 0.7757 (m) cc_final: 0.7502 (p) outliers start: 103 outliers final: 64 residues processed: 386 average time/residue: 0.3109 time to fit residues: 184.2666 Evaluate side-chains 358 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 292 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 203 THR 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 194 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 9 PHE 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 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 162 TYR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 VAL 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 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 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 68 optimal weight: 0.1980 chunk 182 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 75 GLN ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 75 GLN C 250 ASN C 295 GLN C 296 ASN D 42 GLN D 129 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17857 Z= 0.211 Angle : 0.687 9.370 24176 Z= 0.355 Chirality : 0.046 0.310 2757 Planarity : 0.004 0.053 3065 Dihedral : 9.371 77.392 3228 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.75 % Rotamer: Outliers : 3.73 % Allowed : 21.25 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2139 helix: 0.11 (0.27), residues: 333 sheet: -1.25 (0.21), residues: 609 loop : -1.92 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 36 HIS 0.008 0.001 HIS C 18 PHE 0.046 0.002 PHE A 147 TYR 0.021 0.002 TYR D 141 ARG 0.007 0.001 ARG B 76 *********************** 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 409 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 339 time to evaluate : 2.024 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: 0.6772 (t0) cc_final: 0.6415 (t0) REVERT: B 128 GLU cc_start: 0.4518 (tt0) cc_final: 0.3535 (tp30) REVERT: C 62 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6528 (mt-10) REVERT: C 79 PHE cc_start: 0.7558 (m-10) cc_final: 0.6806 (m-80) REVERT: D 32 ARG cc_start: 0.6640 (ptp-170) cc_final: 0.6036 (ptp-170) REVERT: D 37 ASP cc_start: 0.8067 (t0) cc_final: 0.7722 (t70) REVERT: D 69 GLU cc_start: 0.7628 (tt0) cc_final: 0.7308 (pt0) REVERT: D 123 LYS cc_start: 0.7473 (tttp) cc_final: 0.7273 (tttm) REVERT: D 128 GLU cc_start: 0.5902 (tm-30) cc_final: 0.4868 (tt0) REVERT: G 17 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6701 (m170) REVERT: G 311 HIS cc_start: 0.7441 (m90) cc_final: 0.7188 (m90) REVERT: G 320 MET cc_start: 0.8324 (ppp) cc_final: 0.7939 (ppp) REVERT: I 90 ASP cc_start: 0.8061 (m-30) cc_final: 0.7617 (m-30) REVERT: E 55 ASP cc_start: 0.7378 (t0) cc_final: 0.6986 (t0) REVERT: J 18 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.7176 (ttm110) REVERT: J 46 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6121 (mp) REVERT: K 4 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7374 (tmt) REVERT: K 30 SER cc_start: 0.7658 (t) cc_final: 0.7077 (m) REVERT: K 63 SER cc_start: 0.7028 (OUTLIER) cc_final: 0.6573 (m) REVERT: H 103 SER cc_start: 0.7542 (m) cc_final: 0.7225 (p) outliers start: 70 outliers final: 46 residues processed: 383 average time/residue: 0.2949 time to fit residues: 170.7254 Evaluate side-chains 351 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 116 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 197 GLN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 9 PHE 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 111 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain F residue 81 MET 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 48 ILE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 296 ASN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17857 Z= 0.230 Angle : 0.698 8.692 24176 Z= 0.361 Chirality : 0.045 0.290 2757 Planarity : 0.004 0.052 3065 Dihedral : 9.057 75.370 3228 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.27 % Favored : 91.68 % Rotamer: Outliers : 4.31 % Allowed : 21.46 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.17), residues: 2139 helix: 0.19 (0.28), residues: 333 sheet: -1.23 (0.21), residues: 606 loop : -1.92 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP J 35 HIS 0.007 0.001 HIS G 18 PHE 0.033 0.002 PHE A 147 TYR 0.014 0.002 TYR J 86 ARG 0.008 0.001 ARG B 76 *********************** 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 398 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 317 time to evaluate : 2.259 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: 0.6832 (t0) cc_final: 0.6463 (t0) REVERT: A 75 GLN cc_start: 0.7400 (tp40) cc_final: 0.7193 (tt0) REVERT: A 150 ARG cc_start: 0.6497 (mmp80) cc_final: 0.5966 (mmp80) REVERT: B 128 GLU cc_start: 0.4528 (tt0) cc_final: 0.3545 (tp30) REVERT: C 62 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6487 (mt-10) REVERT: C 79 PHE cc_start: 0.7585 (m-10) cc_final: 0.6718 (m-80) REVERT: C 104 ASP cc_start: 0.8384 (t0) cc_final: 0.7903 (t0) REVERT: D 37 ASP cc_start: 0.8073 (t0) cc_final: 0.7718 (t70) REVERT: D 69 GLU cc_start: 0.7629 (tt0) cc_final: 0.7315 (pt0) REVERT: D 123 LYS cc_start: 0.7488 (tttp) cc_final: 0.7260 (tttm) REVERT: D 128 GLU cc_start: 0.5918 (tm-30) cc_final: 0.4872 (tt0) REVERT: D 137 CYS cc_start: 0.5669 (OUTLIER) cc_final: 0.5383 (m) REVERT: D 150 GLU cc_start: 0.7793 (pt0) cc_final: 0.7502 (pt0) REVERT: G 17 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6721 (m170) REVERT: G 85 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7248 (t0) REVERT: G 311 HIS cc_start: 0.7368 (m90) cc_final: 0.7097 (m90) REVERT: G 320 MET cc_start: 0.8356 (ppp) cc_final: 0.7972 (ppp) REVERT: I 90 ASP cc_start: 0.8055 (m-30) cc_final: 0.7846 (m-30) REVERT: E 55 ASP cc_start: 0.7371 (t0) cc_final: 0.6991 (t0) REVERT: J 24 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7384 (mtp85) REVERT: J 30 SER cc_start: 0.7639 (t) cc_final: 0.7086 (m) REVERT: J 46 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6065 (mp) REVERT: J 63 SER cc_start: 0.7173 (t) cc_final: 0.6887 (m) REVERT: K 4 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7419 (tmt) REVERT: K 30 SER cc_start: 0.7708 (t) cc_final: 0.7154 (m) REVERT: H 103 SER cc_start: 0.7530 (m) cc_final: 0.7220 (p) REVERT: L 24 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7215 (mtp85) outliers start: 81 outliers final: 55 residues processed: 370 average time/residue: 0.2915 time to fit residues: 164.3844 Evaluate side-chains 361 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 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 203 THR 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 116 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 98 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 155 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 311 HIS Chi-restraints excluded: chain D residue 9 PHE 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 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain I residue 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 162 TYR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN C 296 ASN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 62 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17857 Z= 0.226 Angle : 0.710 9.875 24176 Z= 0.366 Chirality : 0.045 0.284 2757 Planarity : 0.004 0.053 3065 Dihedral : 8.569 66.286 3228 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 3.78 % Allowed : 22.47 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2139 helix: 0.18 (0.27), residues: 333 sheet: -1.20 (0.21), residues: 606 loop : -1.90 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP H 36 HIS 0.006 0.001 HIS G 18 PHE 0.027 0.002 PHE A 147 TYR 0.013 0.002 TYR C 302 ARG 0.007 0.001 ARG B 76 *********************** 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 389 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 318 time to evaluate : 1.972 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: 0.6799 (t0) cc_final: 0.6418 (t0) REVERT: A 50 GLU cc_start: 0.7695 (tp30) cc_final: 0.7445 (tp30) REVERT: A 75 GLN cc_start: 0.7323 (tp40) cc_final: 0.7084 (tt0) REVERT: A 150 ARG cc_start: 0.6395 (mmp80) cc_final: 0.5897 (mmp80) REVERT: B 46 ASP cc_start: 0.8041 (m-30) cc_final: 0.7716 (m-30) REVERT: B 128 GLU cc_start: 0.4401 (tt0) cc_final: 0.3582 (tp30) REVERT: C 62 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6540 (mt-10) REVERT: C 79 PHE cc_start: 0.7578 (m-10) cc_final: 0.6625 (m-80) REVERT: C 104 ASP cc_start: 0.8287 (t0) cc_final: 0.7844 (t0) REVERT: C 259 LYS cc_start: 0.8415 (tttt) cc_final: 0.8027 (ttpp) REVERT: D 37 ASP cc_start: 0.8039 (t0) cc_final: 0.7680 (t70) REVERT: D 69 GLU cc_start: 0.7596 (tt0) cc_final: 0.7270 (pt0) REVERT: D 123 LYS cc_start: 0.7491 (tttp) cc_final: 0.7278 (tttm) REVERT: D 128 GLU cc_start: 0.5926 (tm-30) cc_final: 0.4867 (tt0) REVERT: G 17 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6768 (m170) REVERT: G 85 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7268 (t0) REVERT: G 311 HIS cc_start: 0.7380 (m90) cc_final: 0.7110 (m90) REVERT: G 320 MET cc_start: 0.8339 (ppp) cc_final: 0.6913 (ppp) REVERT: I 17 MET cc_start: 0.5908 (mmp) cc_final: 0.5240 (mmp) REVERT: I 90 ASP cc_start: 0.8018 (m-30) cc_final: 0.7801 (m-30) REVERT: E 55 ASP cc_start: 0.7419 (t0) cc_final: 0.7031 (t0) REVERT: J 30 SER cc_start: 0.7643 (t) cc_final: 0.7085 (m) REVERT: J 46 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6058 (mp) REVERT: K 4 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7462 (tmt) REVERT: K 30 SER cc_start: 0.7698 (t) cc_final: 0.7153 (m) REVERT: H 70 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6069 (mm) REVERT: H 81 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4624 (mtp) REVERT: L 63 SER cc_start: 0.7265 (t) cc_final: 0.6762 (m) outliers start: 71 outliers final: 57 residues processed: 364 average time/residue: 0.2958 time to fit residues: 162.8449 Evaluate side-chains 363 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 300 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 203 THR 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 116 ASN 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 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 9 PHE 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 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 153 TRP 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 161 VAL Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 115 THR 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 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 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 C 295 GLN D 42 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17857 Z= 0.351 Angle : 0.777 11.731 24176 Z= 0.405 Chirality : 0.048 0.295 2757 Planarity : 0.005 0.056 3065 Dihedral : 8.636 62.538 3228 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.44 % Favored : 90.51 % Rotamer: Outliers : 4.31 % Allowed : 22.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2139 helix: -0.02 (0.27), residues: 333 sheet: -1.33 (0.20), residues: 606 loop : -2.01 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP H 36 HIS 0.008 0.001 HIS G 18 PHE 0.027 0.002 PHE D 63 TYR 0.025 0.002 TYR G 98 ARG 0.006 0.001 ARG L 24 *********************** 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 386 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 1.957 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: 0.7078 (t0) cc_final: 0.6671 (t0) REVERT: A 50 GLU cc_start: 0.7770 (tp30) cc_final: 0.7479 (tp30) REVERT: A 150 ARG cc_start: 0.6608 (mmp80) cc_final: 0.6072 (mmp80) REVERT: B 122 THR cc_start: 0.8562 (m) cc_final: 0.8264 (m) REVERT: B 128 GLU cc_start: 0.4669 (tt0) cc_final: 0.3920 (tp30) REVERT: C 62 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6494 (mt-10) REVERT: C 79 PHE cc_start: 0.7749 (m-10) cc_final: 0.6985 (m-80) REVERT: C 104 ASP cc_start: 0.8362 (t0) cc_final: 0.7908 (t0) REVERT: C 119 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 320 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.6440 (ppp) REVERT: D 32 ARG cc_start: 0.6606 (ptp-170) cc_final: 0.6250 (ptp-170) REVERT: D 37 ASP cc_start: 0.8080 (t0) cc_final: 0.7688 (t70) REVERT: D 69 GLU cc_start: 0.7681 (tt0) cc_final: 0.7394 (pt0) REVERT: D 123 LYS cc_start: 0.7504 (tttp) cc_final: 0.7295 (tttm) REVERT: D 128 GLU cc_start: 0.5869 (tm-30) cc_final: 0.4827 (tt0) REVERT: D 141 TYR cc_start: 0.5783 (t80) cc_final: 0.5466 (t80) REVERT: G 17 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6819 (m170) REVERT: G 85 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7391 (t0) REVERT: G 168 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5828 (tpt) REVERT: G 311 HIS cc_start: 0.7485 (m90) cc_final: 0.7257 (m90) REVERT: G 320 MET cc_start: 0.8327 (ppp) cc_final: 0.6873 (ppp) REVERT: I 17 MET cc_start: 0.5993 (mmp) cc_final: 0.5625 (mmt) REVERT: I 90 ASP cc_start: 0.8063 (m-30) cc_final: 0.7553 (m-30) REVERT: E 36 TRP cc_start: 0.6723 (m100) cc_final: 0.6400 (m-10) REVERT: E 55 ASP cc_start: 0.7457 (t0) cc_final: 0.7119 (t0) REVERT: J 4 MET cc_start: 0.6236 (ttp) cc_final: 0.5511 (ttt) REVERT: J 30 SER cc_start: 0.7846 (t) cc_final: 0.7276 (m) REVERT: J 44 ILE cc_start: 0.5844 (mt) cc_final: 0.5576 (mt) REVERT: J 46 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6209 (mp) REVERT: K 4 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7340 (tmt) REVERT: K 30 SER cc_start: 0.7823 (t) cc_final: 0.7197 (m) REVERT: H 81 MET cc_start: 0.4906 (mtp) cc_final: 0.4613 (mtp) REVERT: L 18 ARG cc_start: 0.7253 (ttt-90) cc_final: 0.6933 (ttm170) outliers start: 81 outliers final: 63 residues processed: 357 average time/residue: 0.3031 time to fit residues: 165.2809 Evaluate side-chains 364 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 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 182 VAL Chi-restraints excluded: chain A residue 203 THR 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 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 168 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 LEU 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 267 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 9 PHE 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 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 168 MET 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 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 70 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 75 GLN D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17857 Z= 0.337 Angle : 0.783 14.375 24176 Z= 0.407 Chirality : 0.047 0.272 2757 Planarity : 0.005 0.055 3065 Dihedral : 8.449 58.217 3228 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.88 % Rotamer: Outliers : 4.10 % Allowed : 22.68 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.17), residues: 2139 helix: -0.29 (0.27), residues: 336 sheet: -1.41 (0.20), residues: 621 loop : -2.09 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP H 36 HIS 0.008 0.001 HIS C 18 PHE 0.025 0.002 PHE D 63 TYR 0.027 0.002 TYR G 98 ARG 0.007 0.001 ARG K 24 ********************** 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 390 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7128 (t0) cc_final: 0.6749 (t0) REVERT: A 150 ARG cc_start: 0.6625 (mmp80) cc_final: 0.6181 (mmp80) REVERT: B 122 THR cc_start: 0.8550 (m) cc_final: 0.8258 (m) REVERT: B 128 GLU cc_start: 0.4781 (tt0) cc_final: 0.4036 (tp30) REVERT: C 62 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6526 (mt-10) REVERT: C 79 PHE cc_start: 0.7722 (m-10) cc_final: 0.6934 (m-80) REVERT: C 104 ASP cc_start: 0.8391 (t0) cc_final: 0.7948 (t0) REVERT: C 119 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: C 320 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.6512 (ppp) REVERT: D 32 ARG cc_start: 0.6617 (ptp-170) cc_final: 0.6221 (ptp-170) REVERT: D 37 ASP cc_start: 0.8114 (t0) cc_final: 0.7725 (t70) REVERT: D 69 GLU cc_start: 0.7650 (tt0) cc_final: 0.7302 (pt0) REVERT: D 128 GLU cc_start: 0.5822 (tm-30) cc_final: 0.4625 (tt0) REVERT: D 141 TYR cc_start: 0.5862 (t80) cc_final: 0.5619 (t80) REVERT: G 17 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6868 (m170) REVERT: G 85 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7429 (t0) REVERT: G 168 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5886 (tpt) REVERT: G 311 HIS cc_start: 0.7559 (m90) cc_final: 0.7313 (m90) REVERT: G 320 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.6911 (ppp) REVERT: I 17 MET cc_start: 0.5985 (mmp) cc_final: 0.5396 (mmt) REVERT: I 90 ASP cc_start: 0.8061 (m-30) cc_final: 0.7582 (m-30) REVERT: I 123 LYS cc_start: 0.7531 (tptt) cc_final: 0.7315 (tttm) REVERT: E 36 TRP cc_start: 0.6792 (m100) cc_final: 0.6549 (m-10) REVERT: E 55 ASP cc_start: 0.7509 (t0) cc_final: 0.7212 (t0) REVERT: J 4 MET cc_start: 0.6397 (ttp) cc_final: 0.5885 (ttt) REVERT: J 30 SER cc_start: 0.7920 (t) cc_final: 0.7403 (m) REVERT: J 44 ILE cc_start: 0.5994 (mt) cc_final: 0.5663 (mt) REVERT: J 46 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6220 (mp) REVERT: F 101 TYR cc_start: 0.6028 (t80) cc_final: 0.5752 (t80) REVERT: K 4 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7441 (tmt) REVERT: K 30 SER cc_start: 0.7868 (t) cc_final: 0.7332 (m) REVERT: H 81 MET cc_start: 0.5288 (mtp) cc_final: 0.4948 (mtp) outliers start: 77 outliers final: 58 residues processed: 365 average time/residue: 0.2877 time to fit residues: 159.2397 Evaluate side-chains 363 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 GLU 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 182 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 THR 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 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 164 LEU 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 267 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 168 MET 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 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 J residue 46 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 115 THR 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 74 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.132984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.116937 restraints weight = 41449.803| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.75 r_work: 0.3828 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17857 Z= 0.356 Angle : 0.810 15.470 24176 Z= 0.421 Chirality : 0.048 0.269 2757 Planarity : 0.005 0.055 3065 Dihedral : 8.388 58.772 3228 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.24 % Favored : 89.71 % Rotamer: Outliers : 3.83 % Allowed : 23.43 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.17), residues: 2139 helix: -0.38 (0.26), residues: 336 sheet: -1.55 (0.20), residues: 627 loop : -2.18 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP L 35 HIS 0.008 0.001 HIS G 18 PHE 0.035 0.002 PHE C 120 TYR 0.026 0.002 TYR G 98 ARG 0.010 0.001 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4264.29 seconds wall clock time: 79 minutes 17.15 seconds (4757.15 seconds total)