Starting phenix.real_space_refine on Fri Nov 15 18:05:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/11_2024/8blb_16105.cif" } resolution = 3.3 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= -0.001 sd= 0.073 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 30 5.16 5 C 6115 2.51 5 N 1515 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9400 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "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: 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: "O" 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: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.18, per 1000 atoms: 0.66 Number of scatterers: 9400 At special positions: 0 Unit cell: (96.9, 94.62, 79.8, 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 30 16.00 O 1740 8.00 N 1515 7.00 C 6115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 14.7% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.871A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 83 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 70 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP C 85 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG C 87 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR C 89 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 91 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER C 62 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE D 70 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP D 85 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR D 68 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG D 87 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE D 66 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR D 89 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR D 91 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER D 62 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR E 83 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE E 70 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP E 85 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR E 68 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG E 87 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE E 66 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR E 89 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR E 91 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER E 62 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1020 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: 2.93 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2855 1.34 - 1.46: 2599 1.46 - 1.58: 4171 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.453 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.70e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12914 1.95 - 3.90: 251 3.90 - 5.86: 20 5.86 - 7.81: 10 7.81 - 9.76: 10 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 119.09 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 119.06 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 119.05 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 5689 25.13 - 50.25: 316 50.25 - 75.38: 35 75.38 - 100.51: 10 100.51 - 125.63: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: dihedral pdb=" C15 VTX A 502 " pdb=" C17 VTX A 502 " pdb=" N16 VTX A 502 " pdb=" C18 VTX A 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.31 -125.63 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX C 502 " pdb=" C17 VTX C 502 " pdb=" N16 VTX C 502 " pdb=" C18 VTX C 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.30 -125.62 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX D 502 " pdb=" C17 VTX D 502 " pdb=" N16 VTX D 502 " pdb=" C18 VTX D 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.29 -125.61 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 892 0.029 - 0.057: 348 0.057 - 0.086: 57 0.086 - 0.115: 135 0.115 - 0.143: 58 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 186 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 170 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 186 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 98 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 99 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 98 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.52e+00 pdb=" N PRO E 99 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 98 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO D 99 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.038 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 362 2.72 - 3.26: 8911 3.26 - 3.81: 14685 3.81 - 4.35: 18995 4.35 - 4.90: 33164 Nonbonded interactions: 76117 Sorted by model distance: nonbonded pdb=" OH TYR D 136 " pdb=" O VAL E 117 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR C 136 " pdb=" O VAL D 117 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG D 219 " pdb=" OE2 GLU D 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG A 219 " pdb=" OE2 GLU A 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG C 219 " pdb=" OE2 GLU C 231 " model vdw 2.298 3.120 ... (remaining 76112 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.140 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.004 0.049 9675 Z= 0.250 Angle : 0.661 9.759 13205 Z= 0.291 Chirality : 0.048 0.143 1490 Planarity : 0.005 0.069 1620 Dihedral : 15.177 125.633 3980 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 1045 helix: -0.07 (0.57), residues: 95 sheet: -0.49 (0.25), residues: 395 loop : -0.63 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 97 HIS 0.001 0.000 HIS A 180 PHE 0.003 0.001 PHE B 125 TYR 0.007 0.001 TYR E 89 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.096 Fit side-chains REVERT: A 239 ARG cc_start: 0.6314 (ptm160) cc_final: 0.4596 (ptt180) REVERT: B 140 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7417 (mtp180) REVERT: B 239 ARG cc_start: 0.6186 (ptm160) cc_final: 0.4666 (ptt180) REVERT: C 103 ASP cc_start: 0.7337 (t70) cc_final: 0.7041 (t0) REVERT: D 103 ASP cc_start: 0.7270 (t70) cc_final: 0.7054 (t0) REVERT: D 212 LEU cc_start: 0.8629 (mt) cc_final: 0.8405 (mt) REVERT: D 239 ARG cc_start: 0.5887 (ptm160) cc_final: 0.5417 (ptm-80) REVERT: E 239 ARG cc_start: 0.6219 (ptm160) cc_final: 0.4521 (ptt180) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3698 time to fit residues: 55.7121 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 152 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9675 Z= 0.202 Angle : 0.631 7.964 13205 Z= 0.325 Chirality : 0.050 0.193 1490 Planarity : 0.005 0.053 1620 Dihedral : 11.379 118.633 1795 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.56 % Allowed : 12.87 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1045 helix: 0.31 (0.55), residues: 95 sheet: -0.34 (0.24), residues: 400 loop : -0.72 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 90 HIS 0.002 0.001 HIS E 180 PHE 0.015 0.001 PHE B 221 TYR 0.011 0.001 TYR D 138 ARG 0.007 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 205 ASN cc_start: 0.7642 (m-40) cc_final: 0.7294 (m-40) REVERT: A 239 ARG cc_start: 0.6133 (ptm160) cc_final: 0.4460 (ptt180) REVERT: B 47 LYS cc_start: 0.9112 (ptmt) cc_final: 0.8899 (ptmt) REVERT: B 107 LYS cc_start: 0.8806 (ptmt) cc_final: 0.8538 (ptmt) REVERT: B 140 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7368 (mtp180) REVERT: B 239 ARG cc_start: 0.6069 (ptm160) cc_final: 0.4575 (ptt180) REVERT: C 56 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7157 (mtm-85) REVERT: C 103 ASP cc_start: 0.7657 (t70) cc_final: 0.7441 (t0) REVERT: C 205 ASN cc_start: 0.7855 (m-40) cc_final: 0.7358 (m-40) REVERT: D 47 LYS cc_start: 0.8917 (ptpp) cc_final: 0.8706 (ptmt) REVERT: D 56 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6850 (mtt90) REVERT: D 103 ASP cc_start: 0.7694 (t70) cc_final: 0.7460 (t0) REVERT: D 212 LEU cc_start: 0.8585 (mt) cc_final: 0.8342 (mt) REVERT: D 239 ARG cc_start: 0.5914 (ptm160) cc_final: 0.5448 (ptm-80) REVERT: E 77 ASN cc_start: 0.8647 (m-40) cc_final: 0.8263 (m110) REVERT: E 197 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7828 (ttmt) REVERT: E 239 ARG cc_start: 0.6356 (ptm160) cc_final: 0.4548 (ptt180) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.3347 time to fit residues: 61.5269 Evaluate side-chains 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9675 Z= 0.217 Angle : 0.597 7.075 13205 Z= 0.304 Chirality : 0.049 0.135 1490 Planarity : 0.005 0.045 1620 Dihedral : 11.286 117.130 1795 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.16 % Allowed : 13.56 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1045 helix: 0.41 (0.56), residues: 95 sheet: -0.62 (0.23), residues: 395 loop : -0.80 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.002 0.001 HIS B 180 PHE 0.010 0.001 PHE E 221 TYR 0.015 0.002 TYR B 45 ARG 0.005 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 205 ASN cc_start: 0.7858 (m-40) cc_final: 0.7607 (m-40) REVERT: A 239 ARG cc_start: 0.6059 (ptm160) cc_final: 0.4418 (ptt180) REVERT: B 78 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 101 ASP cc_start: 0.8130 (t0) cc_final: 0.7858 (t0) REVERT: B 103 ASP cc_start: 0.7708 (t0) cc_final: 0.7492 (t0) REVERT: B 239 ARG cc_start: 0.5885 (ptm160) cc_final: 0.4630 (ptt180) REVERT: C 56 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7626 (mtm-85) REVERT: C 239 ARG cc_start: 0.6142 (ptm160) cc_final: 0.4536 (ptt180) REVERT: D 56 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7264 (mtt90) REVERT: D 64 ASP cc_start: 0.9006 (t0) cc_final: 0.8797 (t70) REVERT: D 103 ASP cc_start: 0.7640 (t70) cc_final: 0.7351 (t0) REVERT: D 200 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7302 (mtp-110) REVERT: D 212 LEU cc_start: 0.8575 (mt) cc_final: 0.8374 (mt) REVERT: D 239 ARG cc_start: 0.5961 (ptm160) cc_final: 0.5602 (ptm-80) REVERT: E 64 ASP cc_start: 0.8964 (t0) cc_final: 0.8425 (t0) REVERT: E 101 ASP cc_start: 0.7848 (t0) cc_final: 0.7417 (t0) REVERT: E 197 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7666 (ttmt) REVERT: E 239 ARG cc_start: 0.6385 (ptm160) cc_final: 0.4577 (ptt180) outliers start: 42 outliers final: 27 residues processed: 177 average time/residue: 0.2790 time to fit residues: 64.9213 Evaluate side-chains 156 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 0.0010 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9675 Z= 0.180 Angle : 0.577 6.580 13205 Z= 0.290 Chirality : 0.048 0.139 1490 Planarity : 0.004 0.042 1620 Dihedral : 11.173 116.002 1795 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.16 % Allowed : 15.74 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1045 helix: 0.32 (0.55), residues: 95 sheet: -0.76 (0.23), residues: 395 loop : -0.75 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.002 0.001 HIS C 180 PHE 0.011 0.001 PHE E 221 TYR 0.012 0.001 TYR B 45 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.239 Fit side-chains REVERT: A 101 ASP cc_start: 0.7841 (t0) cc_final: 0.7340 (t0) REVERT: A 127 ASP cc_start: 0.8261 (t0) cc_final: 0.7953 (t0) REVERT: A 205 ASN cc_start: 0.7801 (m-40) cc_final: 0.7066 (m-40) REVERT: A 239 ARG cc_start: 0.6075 (ptm160) cc_final: 0.4471 (ptt180) REVERT: B 39 ASP cc_start: 0.7945 (m-30) cc_final: 0.7714 (m-30) REVERT: B 78 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8376 (mm-40) REVERT: B 101 ASP cc_start: 0.8115 (t0) cc_final: 0.7723 (t0) REVERT: B 239 ARG cc_start: 0.6017 (ptm160) cc_final: 0.4758 (ptt180) REVERT: C 45 TYR cc_start: 0.7839 (t80) cc_final: 0.7621 (t80) REVERT: C 56 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7886 (mtm-85) REVERT: C 239 ARG cc_start: 0.6053 (ptm160) cc_final: 0.4611 (ptt180) REVERT: D 56 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7636 (mtm-85) REVERT: D 101 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7946 (t0) REVERT: D 103 ASP cc_start: 0.7654 (t70) cc_final: 0.7414 (t0) REVERT: D 239 ARG cc_start: 0.5817 (ptm160) cc_final: 0.5514 (ptm-80) REVERT: E 101 ASP cc_start: 0.7885 (t0) cc_final: 0.7428 (t0) REVERT: E 197 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7455 (mtmt) REVERT: E 239 ARG cc_start: 0.6388 (ptm160) cc_final: 0.4639 (ptt180) outliers start: 42 outliers final: 25 residues processed: 170 average time/residue: 0.2751 time to fit residues: 61.6960 Evaluate side-chains 154 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9675 Z= 0.195 Angle : 0.588 7.847 13205 Z= 0.294 Chirality : 0.049 0.295 1490 Planarity : 0.004 0.038 1620 Dihedral : 11.210 116.369 1795 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.45 % Allowed : 14.75 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.27), residues: 1045 helix: 0.40 (0.56), residues: 95 sheet: -0.98 (0.23), residues: 450 loop : -0.58 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 90 HIS 0.001 0.001 HIS B 180 PHE 0.010 0.001 PHE A 166 TYR 0.011 0.001 TYR B 45 ARG 0.009 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 1.030 Fit side-chains REVERT: A 101 ASP cc_start: 0.7853 (t0) cc_final: 0.7313 (t0) REVERT: A 127 ASP cc_start: 0.8297 (t0) cc_final: 0.8001 (t0) REVERT: A 239 ARG cc_start: 0.6057 (ptm160) cc_final: 0.4438 (ptt180) REVERT: B 101 ASP cc_start: 0.8178 (t0) cc_final: 0.7899 (t0) REVERT: B 107 LYS cc_start: 0.9127 (ptmt) cc_final: 0.8265 (ptmt) REVERT: B 239 ARG cc_start: 0.6029 (ptm160) cc_final: 0.4784 (ptt180) REVERT: C 56 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: C 239 ARG cc_start: 0.6094 (ptm160) cc_final: 0.4618 (ptt180) REVERT: D 56 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7871 (mtm-85) REVERT: D 101 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7941 (t0) REVERT: D 103 ASP cc_start: 0.7671 (t70) cc_final: 0.7406 (t0) REVERT: D 108 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8722 (pt) REVERT: D 239 ARG cc_start: 0.5753 (ptm160) cc_final: 0.4151 (ptt180) REVERT: E 101 ASP cc_start: 0.8009 (t0) cc_final: 0.7596 (t0) REVERT: E 197 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7490 (mtmt) REVERT: E 239 ARG cc_start: 0.6271 (ptm160) cc_final: 0.4564 (ptt180) outliers start: 55 outliers final: 40 residues processed: 197 average time/residue: 0.2538 time to fit residues: 67.1009 Evaluate side-chains 184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 146 GLN C 206 GLN D 78 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9675 Z= 0.250 Angle : 0.610 7.465 13205 Z= 0.307 Chirality : 0.051 0.332 1490 Planarity : 0.005 0.052 1620 Dihedral : 11.385 116.897 1795 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.65 % Allowed : 15.94 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.27), residues: 1045 helix: 0.44 (0.56), residues: 95 sheet: -1.00 (0.23), residues: 450 loop : -0.58 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 85 HIS 0.002 0.001 HIS C 141 PHE 0.012 0.001 PHE D 166 TYR 0.011 0.002 TYR B 45 ARG 0.009 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.084 Fit side-chains REVERT: A 101 ASP cc_start: 0.7889 (t0) cc_final: 0.7331 (t0) REVERT: A 127 ASP cc_start: 0.8274 (t0) cc_final: 0.7990 (t0) REVERT: A 134 ILE cc_start: 0.8317 (mm) cc_final: 0.8070 (mm) REVERT: A 239 ARG cc_start: 0.6066 (ptm160) cc_final: 0.4436 (ptt180) REVERT: B 101 ASP cc_start: 0.8202 (t0) cc_final: 0.7884 (t0) REVERT: B 107 LYS cc_start: 0.9216 (ptmt) cc_final: 0.8393 (ptmt) REVERT: B 239 ARG cc_start: 0.6156 (ptm160) cc_final: 0.4611 (ptt180) REVERT: C 45 TYR cc_start: 0.7990 (t80) cc_final: 0.7613 (t80) REVERT: C 56 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8160 (mtm-85) REVERT: C 239 ARG cc_start: 0.6120 (ptm160) cc_final: 0.4614 (ptt180) REVERT: D 56 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (mtm-85) REVERT: D 101 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7977 (t0) REVERT: D 103 ASP cc_start: 0.7629 (t70) cc_final: 0.7373 (t0) REVERT: D 108 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8685 (pt) REVERT: D 239 ARG cc_start: 0.5807 (ptm160) cc_final: 0.4289 (ptt180) REVERT: E 101 ASP cc_start: 0.8055 (t0) cc_final: 0.7615 (t0) REVERT: E 103 ASP cc_start: 0.7752 (t70) cc_final: 0.7455 (t0) REVERT: E 107 LYS cc_start: 0.9128 (ptmt) cc_final: 0.8717 (ptmt) REVERT: E 197 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7485 (mtmt) REVERT: E 239 ARG cc_start: 0.6061 (ptm160) cc_final: 0.4392 (ptt180) outliers start: 47 outliers final: 40 residues processed: 186 average time/residue: 0.2739 time to fit residues: 66.8633 Evaluate side-chains 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9675 Z= 0.182 Angle : 0.589 7.305 13205 Z= 0.297 Chirality : 0.048 0.202 1490 Planarity : 0.005 0.050 1620 Dihedral : 11.248 116.107 1795 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.55 % Allowed : 16.34 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 1045 helix: 0.62 (0.56), residues: 95 sheet: -1.15 (0.23), residues: 485 loop : -0.47 (0.32), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.002 0.000 HIS C 180 PHE 0.010 0.001 PHE C 221 TYR 0.019 0.001 TYR D 45 ARG 0.006 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 1.104 Fit side-chains REVERT: A 127 ASP cc_start: 0.8273 (t0) cc_final: 0.7996 (t0) REVERT: A 134 ILE cc_start: 0.8319 (mm) cc_final: 0.8073 (mm) REVERT: A 239 ARG cc_start: 0.6037 (ptm160) cc_final: 0.4459 (ptt180) REVERT: B 101 ASP cc_start: 0.8188 (t0) cc_final: 0.7868 (t0) REVERT: B 107 LYS cc_start: 0.9161 (ptmt) cc_final: 0.8356 (ptmt) REVERT: B 239 ARG cc_start: 0.6031 (ptm160) cc_final: 0.4608 (ptt180) REVERT: C 239 ARG cc_start: 0.6068 (ptm160) cc_final: 0.4545 (ptt180) REVERT: D 56 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8130 (mtm-85) REVERT: D 101 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7972 (t0) REVERT: D 103 ASP cc_start: 0.7541 (t70) cc_final: 0.7327 (t0) REVERT: D 108 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (pt) REVERT: D 200 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7383 (mtp-110) REVERT: D 223 MET cc_start: 0.8516 (mmm) cc_final: 0.8276 (mmm) REVERT: D 239 ARG cc_start: 0.5832 (ptm160) cc_final: 0.4354 (ptt180) REVERT: E 101 ASP cc_start: 0.8056 (t0) cc_final: 0.7620 (t0) REVERT: E 103 ASP cc_start: 0.7694 (t70) cc_final: 0.7439 (t0) REVERT: E 107 LYS cc_start: 0.9168 (ptmt) cc_final: 0.8929 (ptmt) REVERT: E 197 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7495 (mtmt) REVERT: E 239 ARG cc_start: 0.6274 (ptm160) cc_final: 0.4500 (ptt180) outliers start: 46 outliers final: 39 residues processed: 182 average time/residue: 0.2561 time to fit residues: 62.5072 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 96 optimal weight: 0.8980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9675 Z= 0.191 Angle : 0.597 10.336 13205 Z= 0.300 Chirality : 0.049 0.191 1490 Planarity : 0.005 0.059 1620 Dihedral : 11.232 116.431 1795 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.26 % Allowed : 17.23 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.27), residues: 1045 helix: 0.66 (0.55), residues: 95 sheet: -1.27 (0.23), residues: 500 loop : -0.36 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.002 0.000 HIS C 180 PHE 0.009 0.001 PHE C 166 TYR 0.018 0.001 TYR D 45 ARG 0.008 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7914 (t0) cc_final: 0.7299 (t0) REVERT: A 127 ASP cc_start: 0.8302 (t0) cc_final: 0.8015 (t0) REVERT: A 134 ILE cc_start: 0.8325 (mm) cc_final: 0.8077 (mm) REVERT: A 239 ARG cc_start: 0.6086 (ptm160) cc_final: 0.4473 (ptt180) REVERT: B 101 ASP cc_start: 0.8185 (t0) cc_final: 0.7883 (t0) REVERT: B 107 LYS cc_start: 0.9183 (ptmt) cc_final: 0.8402 (ptmt) REVERT: B 239 ARG cc_start: 0.6003 (ptm160) cc_final: 0.4562 (ptt180) REVERT: C 45 TYR cc_start: 0.7900 (t80) cc_final: 0.7592 (t80) REVERT: C 204 MET cc_start: 0.7529 (mtt) cc_final: 0.7325 (mtm) REVERT: C 239 ARG cc_start: 0.6084 (ptm160) cc_final: 0.4571 (ptt180) REVERT: D 101 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (t0) REVERT: D 108 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8689 (pt) REVERT: D 223 MET cc_start: 0.8504 (mmm) cc_final: 0.8300 (mmm) REVERT: D 239 ARG cc_start: 0.5806 (ptm160) cc_final: 0.4329 (ptt180) REVERT: E 64 ASP cc_start: 0.8955 (t70) cc_final: 0.8665 (t0) REVERT: E 101 ASP cc_start: 0.8071 (t0) cc_final: 0.7635 (t0) REVERT: E 103 ASP cc_start: 0.7675 (t70) cc_final: 0.7434 (t0) REVERT: E 197 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7549 (mtmt) REVERT: E 204 MET cc_start: 0.7329 (mtt) cc_final: 0.7123 (mtm) REVERT: E 223 MET cc_start: 0.8480 (mmm) cc_final: 0.8255 (mmm) REVERT: E 239 ARG cc_start: 0.6287 (ptm160) cc_final: 0.4641 (ptt180) outliers start: 43 outliers final: 38 residues processed: 182 average time/residue: 0.2595 time to fit residues: 63.3687 Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9675 Z= 0.229 Angle : 0.602 5.943 13205 Z= 0.309 Chirality : 0.049 0.188 1490 Planarity : 0.005 0.053 1620 Dihedral : 11.255 116.868 1795 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.55 % Allowed : 17.33 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.27), residues: 1045 helix: -0.70 (0.47), residues: 125 sheet: -1.31 (0.23), residues: 500 loop : -0.43 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.001 0.000 HIS C 180 PHE 0.008 0.001 PHE E 221 TYR 0.020 0.001 TYR D 45 ARG 0.007 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 1.003 Fit side-chains REVERT: A 101 ASP cc_start: 0.7949 (t0) cc_final: 0.7444 (t0) REVERT: A 127 ASP cc_start: 0.8298 (t0) cc_final: 0.7979 (t0) REVERT: A 134 ILE cc_start: 0.8449 (mm) cc_final: 0.8175 (mm) REVERT: A 239 ARG cc_start: 0.6045 (ptm160) cc_final: 0.4455 (ptt180) REVERT: B 78 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8295 (mm-40) REVERT: B 101 ASP cc_start: 0.8185 (t0) cc_final: 0.7899 (t0) REVERT: B 107 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8363 (ptmt) REVERT: B 239 ARG cc_start: 0.6008 (ptm160) cc_final: 0.4561 (ptt180) REVERT: C 45 TYR cc_start: 0.8043 (t80) cc_final: 0.7762 (t80) REVERT: C 204 MET cc_start: 0.7563 (mtt) cc_final: 0.7312 (mtm) REVERT: C 239 ARG cc_start: 0.6055 (ptm160) cc_final: 0.4596 (ptt180) REVERT: D 101 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7938 (t0) REVERT: D 108 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (pt) REVERT: D 223 MET cc_start: 0.8512 (mmm) cc_final: 0.8308 (mmm) REVERT: D 239 ARG cc_start: 0.5745 (ptm160) cc_final: 0.4308 (ptt180) REVERT: E 101 ASP cc_start: 0.8161 (t0) cc_final: 0.7740 (t0) REVERT: E 103 ASP cc_start: 0.7656 (t70) cc_final: 0.7417 (t0) REVERT: E 197 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7531 (mtmt) REVERT: E 223 MET cc_start: 0.8562 (mmm) cc_final: 0.8329 (mmm) REVERT: E 239 ARG cc_start: 0.6096 (ptm160) cc_final: 0.4489 (ptt180) outliers start: 46 outliers final: 42 residues processed: 168 average time/residue: 0.2675 time to fit residues: 60.6858 Evaluate side-chains 173 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9675 Z= 0.181 Angle : 0.588 5.505 13205 Z= 0.303 Chirality : 0.048 0.192 1490 Planarity : 0.004 0.042 1620 Dihedral : 11.250 116.455 1795 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.06 % Allowed : 18.12 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.27), residues: 1045 helix: -0.64 (0.47), residues: 125 sheet: -1.14 (0.24), residues: 440 loop : -0.65 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.002 0.000 HIS C 180 PHE 0.009 0.001 PHE C 102 TYR 0.017 0.001 TYR D 45 ARG 0.006 0.000 ARG C 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.077 Fit side-chains REVERT: A 101 ASP cc_start: 0.7824 (t0) cc_final: 0.7291 (t0) REVERT: A 127 ASP cc_start: 0.8237 (t0) cc_final: 0.7923 (t0) REVERT: A 197 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7058 (mtpt) REVERT: A 239 ARG cc_start: 0.6129 (ptm160) cc_final: 0.4542 (ptt180) REVERT: B 78 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8307 (mm-40) REVERT: B 101 ASP cc_start: 0.8161 (t0) cc_final: 0.7887 (t0) REVERT: B 107 LYS cc_start: 0.9159 (ptmt) cc_final: 0.8380 (ptmt) REVERT: B 239 ARG cc_start: 0.5968 (ptm160) cc_final: 0.4560 (ptt180) REVERT: C 45 TYR cc_start: 0.7945 (t80) cc_final: 0.7696 (t80) REVERT: C 197 LYS cc_start: 0.7633 (ttmm) cc_final: 0.7175 (mtmt) REVERT: C 223 MET cc_start: 0.8578 (mmm) cc_final: 0.8347 (mmm) REVERT: C 239 ARG cc_start: 0.6027 (ptm160) cc_final: 0.4574 (ptt180) REVERT: D 101 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7886 (t0) REVERT: D 108 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (pt) REVERT: D 239 ARG cc_start: 0.5647 (ptm160) cc_final: 0.4279 (ptt180) REVERT: E 78 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8444 (mm-40) REVERT: E 101 ASP cc_start: 0.8156 (t0) cc_final: 0.7733 (t0) REVERT: E 103 ASP cc_start: 0.7632 (t70) cc_final: 0.7416 (t0) REVERT: E 197 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7573 (mtmt) REVERT: E 223 MET cc_start: 0.8567 (mmm) cc_final: 0.8330 (mmm) REVERT: E 239 ARG cc_start: 0.6262 (ptm160) cc_final: 0.4505 (ptt180) outliers start: 41 outliers final: 38 residues processed: 168 average time/residue: 0.2597 time to fit residues: 58.2683 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 73 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: D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102820 restraints weight = 10940.108| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.10 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9675 Z= 0.197 Angle : 0.593 5.523 13205 Z= 0.305 Chirality : 0.049 0.243 1490 Planarity : 0.004 0.037 1620 Dihedral : 11.292 116.578 1795 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.46 % Allowed : 18.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.27), residues: 1045 helix: -0.64 (0.47), residues: 125 sheet: -1.16 (0.25), residues: 440 loop : -0.69 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 178 HIS 0.001 0.000 HIS C 180 PHE 0.008 0.001 PHE D 221 TYR 0.018 0.001 TYR D 45 ARG 0.006 0.000 ARG D 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.42 seconds wall clock time: 43 minutes 58.50 seconds (2638.50 seconds total)