Starting phenix.real_space_refine on Fri Nov 15 18:08:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bla_16104/11_2024/8bla_16104.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bla_16104/11_2024/8bla_16104.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/8bla_16104/11_2024/8bla_16104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bla_16104/11_2024/8bla_16104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bla_16104/11_2024/8bla_16104.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bla_16104/11_2024/8bla_16104.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= 0.051 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 30 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: 6.27, per 1000 atoms: 0.67 Number of scatterers: 9400 At special positions: 0 Unit cell: (95.45, 95.45, 80.5, 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: 2.81 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: 1.23 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: 6.952A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.702A 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: 6.952A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.684A 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: 3.863A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.676A 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: 6.952A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.952A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.685A 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: 3.863A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.677A 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: 6.952A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.952A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR C 83 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 70 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP C 85 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG C 87 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR C 89 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 91 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 9.685A 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: 3.862A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.677A 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: 6.952A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.702A 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: 6.952A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE D 70 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TRP D 85 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR D 68 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG D 87 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 66 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR D 89 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR D 91 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 9.684A 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: 3.863A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.677A 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: 6.952A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.952A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 83 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE E 70 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP E 85 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 68 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG E 87 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE E 66 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR E 89 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR E 91 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 9.684A 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: 3.862A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.677A 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: 2.95 Time building geometry restraints manager: 3.18 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: 2597 1.46 - 1.58: 4173 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.450 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.448 -0.044 2.00e-02 2.50e+03 4.93e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12899 1.76 - 3.53: 260 3.53 - 5.29: 26 5.29 - 7.06: 10 7.06 - 8.82: 10 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 118.15 -8.82 3.00e+00 1.11e-01 8.64e+00 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 118.15 -8.82 3.00e+00 1.11e-01 8.64e+00 angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 118.14 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 118.14 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 118.13 -8.80 3.00e+00 1.11e-01 8.60e+00 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5724 25.07 - 50.14: 266 50.14 - 75.21: 50 75.21 - 100.28: 10 100.28 - 125.35: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: 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 56.03 -125.35 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C15 VTX B 502 " pdb=" C17 VTX B 502 " pdb=" N16 VTX B 502 " pdb=" C18 VTX B 502 " ideal model delta sinusoidal sigma weight residual -69.32 55.98 -125.30 1 3.00e+01 1.11e-03 1.68e+01 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 55.96 -125.28 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 861 0.029 - 0.058: 380 0.058 - 0.087: 63 0.087 - 0.116: 149 0.116 - 0.145: 37 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 170 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 170 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 170 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 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 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 46 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.20e+00 pdb=" NE ARG A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 46 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 46 " -0.127 9.50e-02 1.11e+02 5.73e-02 2.19e+00 pdb=" NE ARG C 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 46 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 46 " -0.127 9.50e-02 1.11e+02 5.71e-02 2.18e+00 pdb=" NE ARG B 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 46 " -0.002 2.00e-02 2.50e+03 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1417 2.77 - 3.30: 8573 3.30 - 3.83: 15086 3.83 - 4.37: 18431 4.37 - 4.90: 32574 Nonbonded interactions: 76081 Sorted by model distance: nonbonded pdb=" OD2 ASP A 167 " pdb=" NE2 GLN A 169 " model vdw 2.234 3.120 nonbonded pdb=" OD2 ASP B 167 " pdb=" NE2 GLN B 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP D 167 " pdb=" NE2 GLN D 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP E 167 " pdb=" NE2 GLN E 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP C 167 " pdb=" NE2 GLN C 169 " model vdw 2.235 3.120 ... (remaining 76076 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: 0.690 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.460 Find NCS groups from input model: 0.450 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.046 9675 Z= 0.266 Angle : 0.648 8.821 13205 Z= 0.287 Chirality : 0.047 0.145 1490 Planarity : 0.005 0.057 1620 Dihedral : 15.400 125.353 3980 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % 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: -1.26 (0.26), residues: 1045 helix: -0.41 (0.57), residues: 95 sheet: -0.75 (0.24), residues: 395 loop : -0.89 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 190 HIS 0.001 0.000 HIS E 141 PHE 0.007 0.001 PHE C 221 TYR 0.009 0.001 TYR C 89 ARG 0.008 0.001 ARG A 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 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.084 Fit side-chains REVERT: A 149 LYS cc_start: 0.8488 (ptmt) cc_final: 0.7907 (pttt) REVERT: B 46 ARG cc_start: 0.7125 (ptp90) cc_final: 0.6801 (ptm-80) REVERT: B 223 MET cc_start: 0.8159 (mmm) cc_final: 0.7760 (mmt) REVERT: C 46 ARG cc_start: 0.6980 (ptp90) cc_final: 0.6627 (ptm-80) REVERT: C 94 PHE cc_start: 0.8588 (m-10) cc_final: 0.8290 (m-10) REVERT: C 101 ASP cc_start: 0.8807 (t0) cc_final: 0.8588 (t70) REVERT: D 46 ARG cc_start: 0.6991 (ptp90) cc_final: 0.6605 (ptm-80) REVERT: E 46 ARG cc_start: 0.7041 (ptp90) cc_final: 0.6638 (ptm-80) REVERT: E 149 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8025 (pttt) REVERT: E 197 LYS cc_start: 0.7380 (ttpp) cc_final: 0.6816 (ttpt) REVERT: E 232 MET cc_start: 0.8574 (tpp) cc_final: 0.8177 (ttm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2721 time to fit residues: 35.6699 Evaluate side-chains 88 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN C 152 GLN D 152 GLN E 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9675 Z= 0.296 Angle : 0.619 6.823 13205 Z= 0.326 Chirality : 0.050 0.152 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.334 120.901 1795 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.18 % Allowed : 12.48 % Favored : 85.35 % 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: -1.40 (0.26), residues: 1045 helix: 0.07 (0.57), residues: 95 sheet: -1.16 (0.23), residues: 420 loop : -0.78 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 190 HIS 0.002 0.001 HIS E 141 PHE 0.015 0.002 PHE D 221 TYR 0.016 0.002 TYR B 89 ARG 0.002 0.000 ARG C 31 *********************** 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 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.066 Fit side-chains REVERT: A 149 LYS cc_start: 0.8453 (ptmt) cc_final: 0.8069 (pttt) REVERT: B 46 ARG cc_start: 0.7134 (ptp90) cc_final: 0.6906 (ptp90) REVERT: B 232 MET cc_start: 0.8513 (tpp) cc_final: 0.8268 (ttm) REVERT: C 46 ARG cc_start: 0.7150 (ptp90) cc_final: 0.6741 (ptm-80) REVERT: C 232 MET cc_start: 0.8541 (tpp) cc_final: 0.8322 (ttm) REVERT: E 46 ARG cc_start: 0.7196 (ptp90) cc_final: 0.6729 (ptm160) REVERT: E 232 MET cc_start: 0.8542 (tpp) cc_final: 0.8224 (ttm) outliers start: 22 outliers final: 21 residues processed: 112 average time/residue: 0.2669 time to fit residues: 40.2442 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 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 C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 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 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 123 ASN C 123 ASN D 123 ASN E 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9675 Z= 0.155 Angle : 0.540 5.662 13205 Z= 0.282 Chirality : 0.047 0.139 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.893 117.326 1795 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 11.78 % Favored : 86.14 % 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: -1.33 (0.26), residues: 1045 helix: 0.31 (0.56), residues: 95 sheet: -1.13 (0.23), residues: 395 loop : -0.80 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 178 HIS 0.001 0.000 HIS E 141 PHE 0.012 0.001 PHE E 221 TYR 0.011 0.001 TYR B 89 ARG 0.002 0.000 ARG D 140 *********************** 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 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.164 Fit side-chains REVERT: A 56 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8773 (ttm110) REVERT: A 149 LYS cc_start: 0.8425 (ptmt) cc_final: 0.7994 (pttt) REVERT: B 232 MET cc_start: 0.8410 (tpp) cc_final: 0.8124 (ttm) REVERT: C 46 ARG cc_start: 0.7129 (ptp90) cc_final: 0.6666 (ptm160) REVERT: C 130 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8382 (mttp) REVERT: D 56 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7843 (mtm110) REVERT: E 56 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7694 (mtm110) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.2905 time to fit residues: 44.6478 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN E 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9675 Z= 0.164 Angle : 0.526 5.692 13205 Z= 0.272 Chirality : 0.047 0.143 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.846 117.843 1795 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 13.07 % Favored : 83.96 % 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: -1.36 (0.25), residues: 1045 helix: 0.49 (0.57), residues: 95 sheet: -1.14 (0.23), residues: 395 loop : -0.86 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 178 HIS 0.001 0.000 HIS A 141 PHE 0.013 0.001 PHE E 221 TYR 0.012 0.001 TYR B 89 ARG 0.002 0.000 ARG C 56 *********************** 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 1.050 Fit side-chains REVERT: A 56 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8818 (ttm110) REVERT: B 232 MET cc_start: 0.8401 (tpp) cc_final: 0.8163 (ttm) REVERT: C 46 ARG cc_start: 0.6932 (ptp90) cc_final: 0.6540 (ptm160) REVERT: C 130 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8473 (mttp) REVERT: D 56 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: D 93 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8143 (mt-10) REVERT: E 56 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7563 (mtm110) REVERT: E 93 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8250 (mt-10) outliers start: 30 outliers final: 23 residues processed: 130 average time/residue: 0.2529 time to fit residues: 44.4744 Evaluate side-chains 119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG 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 B residue 43 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.1896 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= 0.196 Angle : 0.540 5.821 13205 Z= 0.278 Chirality : 0.047 0.144 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.873 118.620 1795 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.66 % Allowed : 12.38 % Favored : 83.96 % 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: -1.18 (0.25), residues: 1045 helix: 0.64 (0.57), residues: 95 sheet: -0.95 (0.23), residues: 430 loop : -0.78 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.001 0.000 HIS E 141 PHE 0.011 0.001 PHE B 221 TYR 0.013 0.001 TYR D 89 ARG 0.002 0.000 ARG B 56 *********************** 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 137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.120 Fit side-chains REVERT: A 56 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7921 (mtm110) REVERT: B 197 LYS cc_start: 0.7025 (ttpp) cc_final: 0.6526 (ttpt) REVERT: B 232 MET cc_start: 0.8456 (tpp) cc_final: 0.8229 (ttm) REVERT: C 130 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8479 (mttp) REVERT: D 56 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7835 (mtm110) REVERT: D 93 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 197 LYS cc_start: 0.7098 (ttpp) cc_final: 0.6817 (ttmt) REVERT: E 56 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7546 (mtm110) REVERT: E 197 LYS cc_start: 0.6993 (ttpp) cc_final: 0.6496 (ttpt) outliers start: 37 outliers final: 29 residues processed: 133 average time/residue: 0.2629 time to fit residues: 47.1794 Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9675 Z= 0.391 Angle : 0.635 7.671 13205 Z= 0.326 Chirality : 0.051 0.165 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.185 121.141 1795 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.76 % Allowed : 11.98 % Favored : 84.26 % 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: -1.46 (0.25), residues: 1045 helix: 0.89 (0.59), residues: 95 sheet: -1.10 (0.23), residues: 430 loop : -1.10 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.002 0.001 HIS B 180 PHE 0.015 0.002 PHE B 221 TYR 0.020 0.002 TYR D 89 ARG 0.003 0.000 ARG B 56 *********************** 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 133 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.075 Fit side-chains REVERT: A 56 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8067 (mtm110) REVERT: B 184 ASP cc_start: 0.8166 (m-30) cc_final: 0.7495 (m-30) REVERT: B 197 LYS cc_start: 0.7164 (ttpp) cc_final: 0.6822 (ttmm) REVERT: B 232 MET cc_start: 0.8453 (tpp) cc_final: 0.8213 (ttm) REVERT: C 46 ARG cc_start: 0.7178 (ptp90) cc_final: 0.6458 (ptm-80) REVERT: C 130 LYS cc_start: 0.8759 (mmtp) cc_final: 0.8508 (mttp) REVERT: D 56 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7740 (mtm110) REVERT: D 197 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6907 (ttmt) REVERT: D 233 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8016 (mtpp) REVERT: E 56 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8002 (mtm110) REVERT: E 197 LYS cc_start: 0.7205 (ttpp) cc_final: 0.6710 (ttpt) outliers start: 38 outliers final: 31 residues processed: 127 average time/residue: 0.3052 time to fit residues: 49.9739 Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU 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 B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.2128 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= 0.212 Angle : 0.558 6.536 13205 Z= 0.287 Chirality : 0.048 0.150 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.907 119.265 1795 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.56 % Allowed : 11.88 % Favored : 84.55 % 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: -1.42 (0.25), residues: 1045 helix: 0.91 (0.58), residues: 95 sheet: -1.11 (0.23), residues: 430 loop : -1.03 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS D 180 PHE 0.012 0.001 PHE E 221 TYR 0.022 0.001 TYR E 86 ARG 0.004 0.000 ARG A 31 *********************** 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 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 1.077 Fit side-chains REVERT: A 56 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8105 (mtm110) REVERT: C 93 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 130 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8535 (mttp) REVERT: D 56 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7842 (mtm110) REVERT: D 197 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6918 (ttmt) REVERT: D 233 LYS cc_start: 0.8247 (mtpt) cc_final: 0.8001 (mtpp) REVERT: E 46 ARG cc_start: 0.6935 (ptp90) cc_final: 0.6725 (ptp90) REVERT: E 56 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8035 (mtm110) REVERT: E 197 LYS cc_start: 0.7082 (ttpp) cc_final: 0.6589 (ttpt) outliers start: 36 outliers final: 30 residues processed: 127 average time/residue: 0.2917 time to fit residues: 48.4276 Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9675 Z= 0.162 Angle : 0.541 5.716 13205 Z= 0.279 Chirality : 0.047 0.147 1490 Planarity : 0.004 0.027 1620 Dihedral : 10.767 118.024 1795 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.56 % Allowed : 11.88 % Favored : 84.55 % 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: -1.39 (0.25), residues: 1045 helix: 0.76 (0.57), residues: 95 sheet: -1.10 (0.23), residues: 430 loop : -0.98 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 97 HIS 0.002 0.000 HIS E 141 PHE 0.011 0.001 PHE E 94 TYR 0.022 0.001 TYR E 86 ARG 0.003 0.000 ARG A 31 *********************** 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 135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.146 Fit side-chains REVERT: A 56 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8086 (mtm110) REVERT: C 93 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8275 (mt-10) REVERT: C 130 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8559 (mttp) REVERT: D 56 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7852 (mtm110) REVERT: D 197 LYS cc_start: 0.7044 (ttpp) cc_final: 0.6784 (ttmt) REVERT: D 233 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7934 (mtpp) REVERT: E 46 ARG cc_start: 0.6983 (ptp90) cc_final: 0.6764 (ptp90) REVERT: E 56 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.7768 (mtm110) REVERT: E 197 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6542 (ttpt) outliers start: 36 outliers final: 30 residues processed: 130 average time/residue: 0.2802 time to fit residues: 48.1994 Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER 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: 5.9990 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.2250 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= 0.227 Angle : 0.554 6.251 13205 Z= 0.284 Chirality : 0.048 0.150 1490 Planarity : 0.004 0.027 1620 Dihedral : 10.896 119.839 1795 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.66 % Allowed : 11.88 % Favored : 84.46 % 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: -1.43 (0.25), residues: 1045 helix: 0.80 (0.57), residues: 95 sheet: -1.10 (0.23), residues: 430 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 PHE 0.014 0.001 PHE E 94 TYR 0.022 0.001 TYR E 86 ARG 0.004 0.000 ARG A 31 *********************** 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 145 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.999 Fit side-chains REVERT: A 56 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8079 (mtm110) REVERT: B 103 ASP cc_start: 0.8746 (t0) cc_final: 0.8493 (t0) REVERT: C 93 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 130 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8564 (mttp) REVERT: D 56 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7859 (mtm110) REVERT: D 197 LYS cc_start: 0.7052 (ttpp) cc_final: 0.6793 (ttmt) REVERT: D 233 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7941 (mtpp) REVERT: E 56 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.7771 (mtm110) REVERT: E 197 LYS cc_start: 0.7214 (ttpp) cc_final: 0.6561 (ttpt) outliers start: 37 outliers final: 32 residues processed: 139 average time/residue: 0.2772 time to fit residues: 51.0205 Evaluate side-chains 140 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER 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 99 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9675 Z= 0.185 Angle : 0.545 5.904 13205 Z= 0.280 Chirality : 0.047 0.148 1490 Planarity : 0.004 0.031 1620 Dihedral : 10.783 118.777 1795 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.27 % Allowed : 12.28 % Favored : 84.46 % 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: -1.41 (0.25), residues: 1045 helix: 0.79 (0.57), residues: 95 sheet: -1.09 (0.23), residues: 430 loop : -1.02 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.000 HIS E 141 PHE 0.012 0.001 PHE E 94 TYR 0.023 0.001 TYR E 86 ARG 0.008 0.000 ARG B 56 ********************** 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 136 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.014 Fit side-chains REVERT: A 56 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8123 (mtm110) REVERT: B 103 ASP cc_start: 0.8725 (t0) cc_final: 0.8453 (t0) REVERT: C 93 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 56 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7872 (mtm110) REVERT: D 93 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 197 LYS cc_start: 0.7044 (ttpp) cc_final: 0.6779 (ttmt) REVERT: D 233 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7949 (mtpp) REVERT: E 56 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.7740 (mtm110) REVERT: E 197 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6612 (ttpt) outliers start: 33 outliers final: 30 residues processed: 131 average time/residue: 0.2522 time to fit residues: 44.9120 Evaluate side-chains 133 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN 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 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER 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: 5.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.0060 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.100550 restraints weight = 12189.678| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.10 r_work: 0.2927 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2412 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= 0.167 Angle : 0.540 5.767 13205 Z= 0.276 Chirality : 0.047 0.146 1490 Planarity : 0.004 0.039 1620 Dihedral : 10.743 118.273 1795 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.47 % Allowed : 12.38 % Favored : 84.16 % 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: -1.39 (0.25), residues: 1045 helix: 0.85 (0.57), residues: 95 sheet: -1.09 (0.23), residues: 430 loop : -1.00 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 178 HIS 0.002 0.000 HIS E 141 PHE 0.010 0.001 PHE E 221 TYR 0.022 0.001 TYR E 86 ARG 0.009 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.55 seconds wall clock time: 39 minutes 39.88 seconds (2379.88 seconds total)