Starting phenix.real_space_refine on Tue Nov 19 10:06:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/11_2024/7k3b_22655.cif" } resolution = 3.4 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= 0.007 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 81 5.16 5 C 11901 2.51 5 N 3192 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19038 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.05, per 1000 atoms: 0.69 Number of scatterers: 19038 At special positions: 0 Unit cell: (184.87, 186.2, 127.68, 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 81 16.00 O 3864 8.00 N 3192 7.00 C 11901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " 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 ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.5 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 63 sheets defined 16.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 75 through 125 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.244A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.669A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.557A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.689A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.763A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.514A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.697A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.710A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.668A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.578A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (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 39 through 41 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 54 removed outlier: 5.698A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (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 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.044A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.669A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.517A pdb=" N LYS D 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.670A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.646A pdb=" N LYS F 62 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.294A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.601A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL G 138 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU G 184 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU G 140 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 182 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN G 142 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 180 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.291A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.454A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.703A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 191 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 161 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.562A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 17 through 22 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.531A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 160 removed outlier: 4.438A pdb=" N TRP K 153 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 210 " --> pdb=" O VAL K 201 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL L 191 " --> pdb=" O HIS L 174 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 161 through 164 779 hydrogen bonds defined for protein. 1944 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: 7.10 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6038 1.34 - 1.46: 4512 1.46 - 1.58: 8770 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 19434 Sorted by residual: bond pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA O 3 " pdb=" C4 BMA O 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA U 3 " pdb=" C4 BMA U 3 " ideal model delta sigma weight residual 1.541 1.504 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.442 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.441 -0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 19429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 24943 1.46 - 2.92: 1152 2.92 - 4.37: 228 4.37 - 5.83: 55 5.83 - 7.29: 40 Bond angle restraints: 26418 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" N LYS G 195 " pdb=" CA LYS G 195 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLY B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" C GLY F 50 " pdb=" N LYS F 51 " pdb=" CA LYS F 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C GLY D 50 " pdb=" N LYS D 51 " pdb=" CA LYS D 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.79e+00 angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 126.47 -4.93 1.91e+00 2.74e-01 6.65e+00 ... (remaining 26413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 11595 23.02 - 46.04: 572 46.04 - 69.06: 63 69.06 - 92.08: 52 92.08 - 115.10: 24 Dihedral angle restraints: 12306 sinusoidal: 5436 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 37.38 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 40.51 52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA GLN I 81 " pdb=" C GLN I 81 " pdb=" N ALA I 82 " pdb=" CA ALA I 82 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 12303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2631 0.069 - 0.137: 489 0.137 - 0.206: 15 0.206 - 0.274: 15 0.274 - 0.343: 3 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C1 NAG E 401 " pdb=" ND2 ASN E 22 " pdb=" C2 NAG E 401 " pdb=" O5 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 22 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3150 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 194 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO J 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 195 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 194 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO H 195 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 195 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 195 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 194 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO L 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 195 " 0.021 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 867 2.70 - 3.25: 18430 3.25 - 3.80: 31238 3.80 - 4.35: 38786 4.35 - 4.90: 67752 Nonbonded interactions: 157073 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.155 3.040 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.183 3.120 nonbonded pdb=" O SER K 92 " pdb=" OG SER K 100 " model vdw 2.184 3.040 nonbonded pdb=" O SER I 92 " pdb=" OG SER I 100 " model vdw 2.200 3.040 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.202 3.040 ... (remaining 157068 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.780 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: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.960 Find NCS groups from input model: 0.780 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: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.008 0.047 19434 Z= 0.509 Angle : 0.780 7.290 26418 Z= 0.394 Chirality : 0.052 0.343 3153 Planarity : 0.004 0.038 3309 Dihedral : 15.085 115.097 7830 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2352 helix: 2.41 (0.30), residues: 282 sheet: -0.34 (0.18), residues: 771 loop : -0.51 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 153 HIS 0.004 0.001 HIS K 203 PHE 0.019 0.002 PHE I 121 TYR 0.014 0.001 TYR I 178 ARG 0.007 0.001 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 2.159 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 260 MET cc_start: 0.8421 (mmm) cc_final: 0.8187 (mtp) REVERT: A 320 MET cc_start: 0.7235 (ptp) cc_final: 0.7030 (ptp) REVERT: B 67 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7823 (tp30) REVERT: B 77 ILE cc_start: 0.9202 (mm) cc_final: 0.8971 (mp) REVERT: B 86 ASP cc_start: 0.8217 (t0) cc_final: 0.7845 (t0) REVERT: D 67 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7870 (tp30) REVERT: D 74 GLU cc_start: 0.7381 (mp0) cc_final: 0.7037 (mp0) REVERT: F 67 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7595 (tp30) REVERT: F 86 ASP cc_start: 0.8064 (t0) cc_final: 0.7813 (t0) REVERT: F 105 GLN cc_start: 0.8478 (tp40) cc_final: 0.8173 (tp40) REVERT: G 141 LEU cc_start: 0.8417 (mp) cc_final: 0.8107 (mp) REVERT: G 144 PHE cc_start: 0.8354 (p90) cc_final: 0.7902 (p90) REVERT: G 145 TYR cc_start: 0.6973 (t80) cc_final: 0.6652 (t80) REVERT: G 178 TYR cc_start: 0.6600 (m-10) cc_final: 0.6363 (m-10) REVERT: H 164 TRP cc_start: 0.7486 (m100) cc_final: 0.7097 (m100) REVERT: H 205 ILE cc_start: 0.7319 (mp) cc_final: 0.7067 (mp) REVERT: H 210 HIS cc_start: 0.7860 (t-170) cc_final: 0.7333 (t-170) REVERT: H 214 ASN cc_start: 0.7863 (t0) cc_final: 0.7493 (t0) REVERT: H 219 LYS cc_start: 0.7992 (tttm) cc_final: 0.7503 (ttpp) REVERT: I 141 LEU cc_start: 0.8228 (mp) cc_final: 0.7893 (tp) REVERT: I 180 LEU cc_start: 0.8816 (tt) cc_final: 0.8605 (tp) REVERT: J 164 TRP cc_start: 0.7638 (m100) cc_final: 0.6900 (m100) REVERT: J 205 ILE cc_start: 0.7366 (mp) cc_final: 0.6963 (mp) REVERT: J 219 LYS cc_start: 0.7902 (tttm) cc_final: 0.7463 (ttpp) REVERT: K 50 ILE cc_start: 0.9024 (pt) cc_final: 0.8808 (mt) REVERT: K 68 LYS cc_start: 0.8779 (tttt) cc_final: 0.7715 (tptt) REVERT: K 108 LEU cc_start: 0.8969 (mp) cc_final: 0.8431 (tt) REVERT: K 128 GLU cc_start: 0.6997 (mp0) cc_final: 0.6670 (mp0) REVERT: K 150 LYS cc_start: 0.6842 (tppt) cc_final: 0.6412 (tmtt) REVERT: L 132 PHE cc_start: 0.7825 (m-80) cc_final: 0.7435 (m-10) REVERT: L 153 LYS cc_start: 0.7750 (tptm) cc_final: 0.6846 (tptt) REVERT: L 164 TRP cc_start: 0.7412 (m100) cc_final: 0.6513 (m100) REVERT: L 179 VAL cc_start: 0.8917 (t) cc_final: 0.8680 (p) REVERT: L 205 ILE cc_start: 0.7300 (mp) cc_final: 0.6665 (mp) REVERT: L 210 HIS cc_start: 0.7432 (t-170) cc_final: 0.7220 (t-170) REVERT: L 219 LYS cc_start: 0.7904 (tttm) cc_final: 0.7590 (ttpp) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3682 time to fit residues: 226.4878 Evaluate side-chains 277 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN E 197 GLN E 322 ASN G 53 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19434 Z= 0.213 Angle : 0.626 8.470 26418 Z= 0.313 Chirality : 0.048 0.359 3153 Planarity : 0.004 0.045 3309 Dihedral : 10.848 80.001 3573 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 8.24 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2352 helix: 2.63 (0.30), residues: 282 sheet: -0.28 (0.18), residues: 780 loop : -0.54 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 153 HIS 0.004 0.001 HIS E 184 PHE 0.018 0.001 PHE I 123 TYR 0.024 0.001 TYR K 178 ARG 0.004 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7197 (tt0) cc_final: 0.6300 (tt0) REVERT: A 208 ARG cc_start: 0.7341 (ptp-170) cc_final: 0.7074 (ptp-170) REVERT: A 320 MET cc_start: 0.6970 (ptp) cc_final: 0.6556 (ptp) REVERT: A 322 ASN cc_start: 0.6433 (t0) cc_final: 0.6086 (t0) REVERT: B 86 ASP cc_start: 0.8082 (t0) cc_final: 0.7732 (t0) REVERT: C 260 MET cc_start: 0.8292 (mtp) cc_final: 0.7896 (mtp) REVERT: D 67 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7878 (tp30) REVERT: D 74 GLU cc_start: 0.7539 (mp0) cc_final: 0.7167 (mp0) REVERT: D 85 GLU cc_start: 0.8437 (tp30) cc_final: 0.8236 (tp30) REVERT: F 67 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7538 (tp30) REVERT: F 74 GLU cc_start: 0.7429 (mp0) cc_final: 0.7154 (mp0) REVERT: F 86 ASP cc_start: 0.8006 (t0) cc_final: 0.7726 (t0) REVERT: F 105 GLN cc_start: 0.8397 (tp40) cc_final: 0.8136 (tp40) REVERT: F 115 MET cc_start: 0.6814 (ttt) cc_final: 0.6499 (mtp) REVERT: G 141 LEU cc_start: 0.8406 (mp) cc_final: 0.8064 (mp) REVERT: G 144 PHE cc_start: 0.8363 (p90) cc_final: 0.7896 (p90) REVERT: G 145 TYR cc_start: 0.6938 (t80) cc_final: 0.6624 (t80) REVERT: H 89 ASP cc_start: 0.8835 (p0) cc_final: 0.8053 (p0) REVERT: H 205 ILE cc_start: 0.7372 (mp) cc_final: 0.7013 (mp) REVERT: H 210 HIS cc_start: 0.7117 (t-170) cc_final: 0.6796 (t-170) REVERT: H 214 ASN cc_start: 0.8050 (t0) cc_final: 0.7796 (t0) REVERT: I 87 ASP cc_start: 0.8324 (t0) cc_final: 0.7992 (t0) REVERT: I 141 LEU cc_start: 0.8028 (mp) cc_final: 0.7759 (tp) REVERT: J 83 MET cc_start: 0.7895 (mtp) cc_final: 0.7597 (mtp) REVERT: J 90 ASP cc_start: 0.8837 (m-30) cc_final: 0.8614 (m-30) REVERT: J 164 TRP cc_start: 0.7624 (m100) cc_final: 0.7018 (m100) REVERT: J 205 ILE cc_start: 0.7045 (mp) cc_final: 0.6532 (mm) REVERT: J 210 HIS cc_start: 0.6984 (t-170) cc_final: 0.6747 (t-170) REVERT: K 107 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8316 (mtmm) REVERT: K 108 LEU cc_start: 0.8976 (mp) cc_final: 0.8560 (tt) REVERT: K 128 GLU cc_start: 0.7154 (mp0) cc_final: 0.6909 (mp0) REVERT: K 141 LEU cc_start: 0.8326 (mp) cc_final: 0.7786 (tp) REVERT: L 83 MET cc_start: 0.7834 (mtp) cc_final: 0.7599 (ttm) REVERT: L 164 TRP cc_start: 0.7477 (m100) cc_final: 0.6145 (m100) REVERT: L 179 VAL cc_start: 0.8879 (t) cc_final: 0.8658 (p) REVERT: L 205 ILE cc_start: 0.7305 (mp) cc_final: 0.6818 (mm) outliers start: 25 outliers final: 17 residues processed: 342 average time/residue: 0.3193 time to fit residues: 166.0012 Evaluate side-chains 299 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS H 181 GLN I 157 ASN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 ASN J 181 GLN K 39 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 19434 Z= 0.512 Angle : 0.735 11.189 26418 Z= 0.365 Chirality : 0.051 0.372 3153 Planarity : 0.004 0.042 3309 Dihedral : 10.063 75.390 3573 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.92 % Allowed : 11.93 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2352 helix: 2.45 (0.31), residues: 279 sheet: -0.42 (0.18), residues: 780 loop : -0.75 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 164 HIS 0.008 0.002 HIS K 203 PHE 0.019 0.002 PHE E 87 TYR 0.025 0.002 TYR K 178 ARG 0.011 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 2.095 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 35 GLU cc_start: 0.7264 (tt0) cc_final: 0.6279 (tt0) REVERT: A 189 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 320 MET cc_start: 0.7098 (ptp) cc_final: 0.6794 (ptp) REVERT: A 322 ASN cc_start: 0.6536 (t0) cc_final: 0.6231 (t0) REVERT: B 86 ASP cc_start: 0.8042 (t0) cc_final: 0.7607 (t0) REVERT: B 114 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7200 (tm-30) REVERT: C 123 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7871 (mt-10) REVERT: C 197 GLN cc_start: 0.8751 (mp10) cc_final: 0.8248 (mp10) REVERT: C 260 MET cc_start: 0.8495 (mtp) cc_final: 0.8068 (mtp) REVERT: E 31 ASP cc_start: 0.7573 (m-30) cc_final: 0.7258 (m-30) REVERT: F 67 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7660 (tp30) REVERT: F 76 ARG cc_start: 0.8903 (mtp180) cc_final: 0.8577 (mtp180) REVERT: F 86 ASP cc_start: 0.8067 (t0) cc_final: 0.7685 (t0) REVERT: F 105 GLN cc_start: 0.8813 (tp40) cc_final: 0.8513 (tp40) REVERT: F 115 MET cc_start: 0.6613 (ttt) cc_final: 0.6277 (mtp) REVERT: G 53 ASN cc_start: 0.6644 (t160) cc_final: 0.6400 (t0) REVERT: G 128 GLU cc_start: 0.7512 (pm20) cc_final: 0.7188 (pm20) REVERT: G 145 TYR cc_start: 0.7080 (t80) cc_final: 0.6652 (t80) REVERT: G 153 TRP cc_start: 0.5382 (m100) cc_final: 0.4986 (m100) REVERT: H 210 HIS cc_start: 0.7600 (t-170) cc_final: 0.7132 (t-170) REVERT: H 214 ASN cc_start: 0.8082 (t0) cc_final: 0.7746 (t0) REVERT: I 87 ASP cc_start: 0.8356 (t0) cc_final: 0.7988 (t0) REVERT: I 141 LEU cc_start: 0.8238 (mp) cc_final: 0.8003 (tp) REVERT: J 83 MET cc_start: 0.8265 (mtp) cc_final: 0.7739 (mtp) REVERT: J 148 LEU cc_start: 0.8390 (mt) cc_final: 0.7876 (tp) REVERT: J 164 TRP cc_start: 0.7760 (m100) cc_final: 0.6905 (m100) REVERT: J 205 ILE cc_start: 0.7044 (mp) cc_final: 0.6628 (mm) REVERT: K 68 LYS cc_start: 0.8892 (tttt) cc_final: 0.7786 (tptt) REVERT: K 108 LEU cc_start: 0.8996 (mp) cc_final: 0.8413 (tt) REVERT: K 128 GLU cc_start: 0.7005 (mp0) cc_final: 0.6480 (mp0) REVERT: K 215 ASN cc_start: 0.6991 (t0) cc_final: 0.6255 (m-40) REVERT: L 132 PHE cc_start: 0.8003 (m-10) cc_final: 0.7482 (m-10) REVERT: L 179 VAL cc_start: 0.8731 (t) cc_final: 0.8377 (p) outliers start: 40 outliers final: 31 residues processed: 315 average time/residue: 0.3241 time to fit residues: 154.7653 Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS I 171 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19434 Z= 0.300 Angle : 0.647 9.803 26418 Z= 0.319 Chirality : 0.049 0.360 3153 Planarity : 0.004 0.040 3309 Dihedral : 9.214 68.032 3573 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.96 % Allowed : 13.51 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2352 helix: 2.63 (0.31), residues: 279 sheet: -0.29 (0.18), residues: 762 loop : -0.72 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 164 HIS 0.010 0.001 HIS I 36 PHE 0.013 0.001 PHE E 87 TYR 0.028 0.001 TYR K 178 ARG 0.005 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 2.233 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: B 114 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7193 (tm-30) REVERT: C 35 GLU cc_start: 0.7022 (tt0) cc_final: 0.6581 (tt0) REVERT: C 168 MET cc_start: 0.8484 (mmm) cc_final: 0.8259 (mmm) REVERT: C 195 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: C 197 GLN cc_start: 0.8774 (mp10) cc_final: 0.8306 (mp10) REVERT: C 260 MET cc_start: 0.8473 (mtp) cc_final: 0.8072 (mtp) REVERT: E 35 GLU cc_start: 0.7379 (tt0) cc_final: 0.6617 (tt0) REVERT: F 67 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7599 (tp30) REVERT: F 86 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t0) REVERT: F 105 GLN cc_start: 0.8790 (tp40) cc_final: 0.8539 (tp40) REVERT: F 115 MET cc_start: 0.6569 (ttt) cc_final: 0.6298 (mtp) REVERT: G 53 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6746 (t0) REVERT: G 145 TYR cc_start: 0.7084 (t80) cc_final: 0.6690 (t80) REVERT: G 153 TRP cc_start: 0.5353 (m100) cc_final: 0.4910 (m100) REVERT: I 87 ASP cc_start: 0.8264 (t0) cc_final: 0.7871 (t0) REVERT: I 141 LEU cc_start: 0.8086 (mp) cc_final: 0.7834 (tp) REVERT: J 83 MET cc_start: 0.8264 (mtp) cc_final: 0.7947 (mtp) REVERT: J 123 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8807 (p) REVERT: J 148 LEU cc_start: 0.8460 (mt) cc_final: 0.8118 (tp) REVERT: J 164 TRP cc_start: 0.7872 (m100) cc_final: 0.7632 (m100) REVERT: J 205 ILE cc_start: 0.7208 (mp) cc_final: 0.6672 (mm) REVERT: K 108 LEU cc_start: 0.8990 (mp) cc_final: 0.8476 (tt) REVERT: K 215 ASN cc_start: 0.6851 (t0) cc_final: 0.6621 (m-40) REVERT: L 83 MET cc_start: 0.7903 (mtp) cc_final: 0.7546 (mtp) REVERT: L 132 PHE cc_start: 0.7970 (m-10) cc_final: 0.7586 (m-10) REVERT: L 179 VAL cc_start: 0.8746 (t) cc_final: 0.8477 (p) outliers start: 41 outliers final: 32 residues processed: 312 average time/residue: 0.3318 time to fit residues: 157.7099 Evaluate side-chains 305 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN E 322 ASN G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19434 Z= 0.424 Angle : 0.689 9.240 26418 Z= 0.341 Chirality : 0.050 0.371 3153 Planarity : 0.004 0.041 3309 Dihedral : 8.791 62.825 3573 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.87 % Allowed : 13.70 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2352 helix: 2.52 (0.30), residues: 279 sheet: -0.38 (0.18), residues: 768 loop : -0.83 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 164 HIS 0.011 0.001 HIS I 36 PHE 0.016 0.002 PHE K 121 TYR 0.017 0.002 TYR I 145 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7124 (tm-30) REVERT: C 195 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: C 197 GLN cc_start: 0.8803 (mp10) cc_final: 0.8346 (mp10) REVERT: C 260 MET cc_start: 0.8514 (mtp) cc_final: 0.8153 (mtp) REVERT: F 67 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7715 (tp30) REVERT: F 86 ASP cc_start: 0.8045 (t0) cc_final: 0.7720 (t0) REVERT: F 105 GLN cc_start: 0.8858 (tp40) cc_final: 0.8586 (tp40) REVERT: F 115 MET cc_start: 0.6608 (ttt) cc_final: 0.6310 (mtp) REVERT: G 53 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6774 (t0) REVERT: G 144 PHE cc_start: 0.8290 (p90) cc_final: 0.7899 (p90) REVERT: G 153 TRP cc_start: 0.5387 (m100) cc_final: 0.4950 (m100) REVERT: H 148 LEU cc_start: 0.8462 (tp) cc_final: 0.8032 (tp) REVERT: H 205 ILE cc_start: 0.8013 (mp) cc_final: 0.7377 (mm) REVERT: H 214 ASN cc_start: 0.8220 (t0) cc_final: 0.7895 (t0) REVERT: I 87 ASP cc_start: 0.8343 (t0) cc_final: 0.7946 (t0) REVERT: I 141 LEU cc_start: 0.8136 (mp) cc_final: 0.7899 (tp) REVERT: I 145 TYR cc_start: 0.6002 (t80) cc_final: 0.5696 (t80) REVERT: J 123 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8822 (p) REVERT: J 148 LEU cc_start: 0.8443 (mt) cc_final: 0.8133 (tp) REVERT: J 205 ILE cc_start: 0.7335 (mp) cc_final: 0.6730 (mp) REVERT: K 68 LYS cc_start: 0.8869 (tttt) cc_final: 0.7822 (tptt) REVERT: K 108 LEU cc_start: 0.8999 (mp) cc_final: 0.8390 (tt) REVERT: K 141 LEU cc_start: 0.8244 (mp) cc_final: 0.7585 (tp) REVERT: K 215 ASN cc_start: 0.7458 (t0) cc_final: 0.6856 (t0) REVERT: L 83 MET cc_start: 0.8135 (mtp) cc_final: 0.7615 (mtp) REVERT: L 132 PHE cc_start: 0.7953 (m-10) cc_final: 0.7433 (m-10) REVERT: L 179 VAL cc_start: 0.8635 (t) cc_final: 0.8404 (p) outliers start: 60 outliers final: 45 residues processed: 311 average time/residue: 0.2983 time to fit residues: 145.2276 Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 322 ASN G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19434 Z= 0.265 Angle : 0.641 9.837 26418 Z= 0.317 Chirality : 0.048 0.363 3153 Planarity : 0.004 0.037 3309 Dihedral : 8.249 57.362 3573 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 14.89 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2352 helix: 2.73 (0.31), residues: 279 sheet: -0.37 (0.19), residues: 747 loop : -0.82 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 164 HIS 0.012 0.001 HIS I 36 PHE 0.011 0.001 PHE E 87 TYR 0.019 0.001 TYR C 257 ARG 0.003 0.000 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: C 260 MET cc_start: 0.8461 (mtp) cc_final: 0.8096 (mtp) REVERT: D 115 MET cc_start: 0.6198 (mtt) cc_final: 0.5975 (mtt) REVERT: F 67 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7605 (tp30) REVERT: F 86 ASP cc_start: 0.8035 (t0) cc_final: 0.7779 (t0) REVERT: F 105 GLN cc_start: 0.8873 (tp40) cc_final: 0.8658 (tp40) REVERT: F 115 MET cc_start: 0.6582 (ttt) cc_final: 0.6323 (mtp) REVERT: G 53 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7131 (t0) REVERT: G 153 TRP cc_start: 0.5352 (m100) cc_final: 0.4939 (m100) REVERT: H 148 LEU cc_start: 0.8439 (tp) cc_final: 0.8027 (tp) REVERT: I 87 ASP cc_start: 0.8271 (t0) cc_final: 0.7872 (t0) REVERT: I 141 LEU cc_start: 0.8121 (mp) cc_final: 0.7885 (tp) REVERT: J 148 LEU cc_start: 0.8414 (mt) cc_final: 0.8131 (tp) REVERT: K 50 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9021 (mp) REVERT: K 68 LYS cc_start: 0.8841 (tttt) cc_final: 0.7750 (tptt) REVERT: K 108 LEU cc_start: 0.9015 (mp) cc_final: 0.8461 (tt) REVERT: K 141 LEU cc_start: 0.8275 (mp) cc_final: 0.7643 (tp) REVERT: K 215 ASN cc_start: 0.7495 (t0) cc_final: 0.6911 (t0) REVERT: L 83 MET cc_start: 0.8102 (mtp) cc_final: 0.7576 (mtp) REVERT: L 132 PHE cc_start: 0.7939 (m-10) cc_final: 0.7467 (m-10) outliers start: 53 outliers final: 41 residues processed: 307 average time/residue: 0.2996 time to fit residues: 144.0670 Evaluate side-chains 304 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 126 optimal weight: 0.2980 chunk 225 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19434 Z= 0.218 Angle : 0.620 9.207 26418 Z= 0.308 Chirality : 0.048 0.360 3153 Planarity : 0.004 0.045 3309 Dihedral : 7.675 56.135 3573 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.59 % Allowed : 15.52 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2352 helix: 2.85 (0.31), residues: 279 sheet: -0.26 (0.19), residues: 747 loop : -0.80 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 164 HIS 0.010 0.001 HIS I 36 PHE 0.011 0.001 PHE J 132 TYR 0.026 0.001 TYR G 145 ARG 0.008 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 GLU cc_start: 0.8561 (tp30) cc_final: 0.8244 (tp30) REVERT: B 86 ASP cc_start: 0.7935 (t0) cc_final: 0.7559 (t0) REVERT: C 195 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: C 260 MET cc_start: 0.8475 (mtp) cc_final: 0.8131 (mtp) REVERT: D 85 GLU cc_start: 0.8321 (tp30) cc_final: 0.8065 (tp30) REVERT: F 67 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7549 (tp30) REVERT: F 86 ASP cc_start: 0.8017 (t0) cc_final: 0.7757 (t0) REVERT: F 105 GLN cc_start: 0.8860 (tp40) cc_final: 0.8638 (tp40) REVERT: F 115 MET cc_start: 0.6507 (ttt) cc_final: 0.6280 (mtp) REVERT: G 153 TRP cc_start: 0.5316 (m100) cc_final: 0.4900 (m100) REVERT: H 148 LEU cc_start: 0.8470 (tp) cc_final: 0.7982 (tp) REVERT: I 87 ASP cc_start: 0.8277 (t0) cc_final: 0.7862 (t0) REVERT: I 141 LEU cc_start: 0.8101 (mp) cc_final: 0.7873 (tp) REVERT: I 212 LYS cc_start: 0.5830 (tppp) cc_final: 0.5481 (ttmt) REVERT: J 148 LEU cc_start: 0.8352 (mt) cc_final: 0.8093 (tp) REVERT: K 50 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9022 (mp) REVERT: K 108 LEU cc_start: 0.9012 (mp) cc_final: 0.8472 (tt) REVERT: K 141 LEU cc_start: 0.8259 (mp) cc_final: 0.7625 (tp) REVERT: K 215 ASN cc_start: 0.7313 (t0) cc_final: 0.6855 (t0) REVERT: L 83 MET cc_start: 0.8084 (mtp) cc_final: 0.7580 (mtp) REVERT: L 118 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8779 (pt0) REVERT: L 132 PHE cc_start: 0.7901 (m-10) cc_final: 0.7474 (m-10) outliers start: 54 outliers final: 40 residues processed: 302 average time/residue: 0.3012 time to fit residues: 142.5440 Evaluate side-chains 301 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 0.2980 chunk 205 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19434 Z= 0.238 Angle : 0.626 9.198 26418 Z= 0.311 Chirality : 0.048 0.366 3153 Planarity : 0.004 0.036 3309 Dihedral : 7.290 56.438 3573 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.63 % Allowed : 15.85 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2352 helix: 2.90 (0.30), residues: 279 sheet: -0.19 (0.19), residues: 708 loop : -0.80 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP J 164 HIS 0.010 0.001 HIS I 36 PHE 0.010 0.001 PHE J 132 TYR 0.022 0.001 TYR G 145 ARG 0.007 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7938 (t0) cc_final: 0.7540 (t0) REVERT: C 195 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: C 260 MET cc_start: 0.8480 (mtp) cc_final: 0.8134 (mtp) REVERT: C 262 THR cc_start: 0.8539 (m) cc_final: 0.8327 (t) REVERT: C 295 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8733 (pp30) REVERT: F 67 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7541 (tp30) REVERT: F 86 ASP cc_start: 0.8027 (t0) cc_final: 0.7686 (t0) REVERT: G 153 TRP cc_start: 0.5290 (m100) cc_final: 0.4907 (m100) REVERT: H 148 LEU cc_start: 0.8314 (tp) cc_final: 0.7910 (tp) REVERT: I 87 ASP cc_start: 0.8272 (t0) cc_final: 0.7847 (t0) REVERT: I 141 LEU cc_start: 0.8072 (mp) cc_final: 0.7834 (tp) REVERT: I 212 LYS cc_start: 0.5828 (tppp) cc_final: 0.5481 (ttmt) REVERT: J 148 LEU cc_start: 0.8520 (mt) cc_final: 0.8293 (tp) REVERT: K 108 LEU cc_start: 0.8998 (mp) cc_final: 0.8466 (tt) REVERT: K 215 ASN cc_start: 0.6991 (t0) cc_final: 0.6568 (t0) REVERT: L 83 MET cc_start: 0.8116 (mtp) cc_final: 0.7569 (mtp) REVERT: L 118 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8610 (pt0) REVERT: L 132 PHE cc_start: 0.8019 (m-10) cc_final: 0.7616 (m-10) outliers start: 55 outliers final: 44 residues processed: 299 average time/residue: 0.3608 time to fit residues: 170.8260 Evaluate side-chains 303 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 0.0060 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19434 Z= 0.225 Angle : 0.622 9.159 26418 Z= 0.310 Chirality : 0.048 0.360 3153 Planarity : 0.004 0.036 3309 Dihedral : 7.040 56.203 3573 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.73 % Allowed : 16.19 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2352 helix: 2.91 (0.30), residues: 279 sheet: -0.03 (0.19), residues: 744 loop : -0.80 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP J 164 HIS 0.009 0.001 HIS I 36 PHE 0.010 0.001 PHE J 132 TYR 0.018 0.001 TYR G 145 ARG 0.007 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7919 (t0) cc_final: 0.7484 (t0) REVERT: C 195 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: C 260 MET cc_start: 0.8476 (mtp) cc_final: 0.8124 (mtp) REVERT: C 262 THR cc_start: 0.8502 (m) cc_final: 0.8247 (t) REVERT: C 295 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8731 (pp30) REVERT: D 85 GLU cc_start: 0.8301 (tp30) cc_final: 0.8099 (tp30) REVERT: F 67 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7534 (tp30) REVERT: F 86 ASP cc_start: 0.8043 (t0) cc_final: 0.7690 (t0) REVERT: F 105 GLN cc_start: 0.8881 (tp40) cc_final: 0.8648 (tp40) REVERT: G 153 TRP cc_start: 0.5314 (m100) cc_final: 0.4913 (m100) REVERT: H 126 SER cc_start: 0.7836 (m) cc_final: 0.7202 (t) REVERT: I 87 ASP cc_start: 0.8252 (t0) cc_final: 0.7801 (t0) REVERT: I 141 LEU cc_start: 0.8064 (mp) cc_final: 0.7825 (tp) REVERT: I 212 LYS cc_start: 0.5826 (tppp) cc_final: 0.5492 (ttmt) REVERT: J 148 LEU cc_start: 0.8552 (mt) cc_final: 0.8312 (tp) REVERT: K 108 LEU cc_start: 0.9002 (mp) cc_final: 0.8456 (tt) REVERT: K 141 LEU cc_start: 0.8281 (mp) cc_final: 0.7643 (tp) REVERT: K 215 ASN cc_start: 0.7057 (t0) cc_final: 0.6592 (t0) REVERT: L 118 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: L 132 PHE cc_start: 0.8042 (m-10) cc_final: 0.7508 (m-10) outliers start: 57 outliers final: 46 residues processed: 305 average time/residue: 0.2922 time to fit residues: 140.2579 Evaluate side-chains 310 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 214 optimal weight: 0.4980 chunk 185 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS K 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19434 Z= 0.208 Angle : 0.613 9.205 26418 Z= 0.306 Chirality : 0.047 0.354 3153 Planarity : 0.004 0.036 3309 Dihedral : 6.777 57.681 3573 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.39 % Allowed : 16.71 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2352 helix: 2.97 (0.30), residues: 279 sheet: 0.06 (0.19), residues: 714 loop : -0.85 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP J 164 HIS 0.009 0.001 HIS I 36 PHE 0.010 0.001 PHE D 63 TYR 0.017 0.001 TYR G 145 ARG 0.006 0.000 ARG I 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6507 (ttp) REVERT: C 195 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: C 260 MET cc_start: 0.8434 (mtp) cc_final: 0.8083 (mtp) REVERT: C 262 THR cc_start: 0.8479 (m) cc_final: 0.8238 (t) REVERT: C 295 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8693 (pp30) REVERT: F 67 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7564 (tp30) REVERT: F 86 ASP cc_start: 0.8009 (t0) cc_final: 0.7678 (t0) REVERT: G 144 PHE cc_start: 0.7896 (p90) cc_final: 0.7617 (p90) REVERT: G 153 TRP cc_start: 0.5290 (m100) cc_final: 0.4891 (m100) REVERT: H 126 SER cc_start: 0.7720 (m) cc_final: 0.7070 (t) REVERT: I 87 ASP cc_start: 0.8243 (t0) cc_final: 0.7832 (t0) REVERT: I 141 LEU cc_start: 0.8028 (mp) cc_final: 0.7800 (tp) REVERT: I 212 LYS cc_start: 0.5791 (tppp) cc_final: 0.5559 (ttmt) REVERT: J 148 LEU cc_start: 0.8457 (mt) cc_final: 0.8238 (tp) REVERT: J 207 ASN cc_start: 0.6929 (p0) cc_final: 0.6607 (t0) REVERT: K 108 LEU cc_start: 0.8997 (mp) cc_final: 0.8449 (tt) REVERT: K 141 LEU cc_start: 0.8259 (mp) cc_final: 0.7628 (tp) REVERT: K 215 ASN cc_start: 0.7369 (t0) cc_final: 0.6932 (t0) REVERT: L 118 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8617 (pt0) REVERT: L 132 PHE cc_start: 0.8030 (m-10) cc_final: 0.7735 (m-80) outliers start: 50 outliers final: 42 residues processed: 298 average time/residue: 0.2574 time to fit residues: 121.1745 Evaluate side-chains 306 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 171 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 185 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: