Starting phenix.real_space_refine on Fri Dec 27 12:19:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqb_33392/12_2024/7xqb_33392_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 15996 2.51 5 N 3144 2.21 5 O 3564 1.98 5 H 20040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42852 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "G" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "B" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "C" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "F" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "I" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "J" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "K" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "L" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3315 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "G" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "C" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 242 Unusual residues: {'C14': 10, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "D" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 270 Unusual residues: {'C14': 12, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "F" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "H" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "I" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "K" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 256 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 16.83, per 1000 atoms: 0.39 Number of scatterers: 42852 At special positions: 0 Unit cell: (108, 112.725, 185.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 O 3564 8.00 N 3144 7.00 C 15996 6.00 H 20040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " 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 Time building additional restraints: 8.10 Conformation dependent library (CDL) restraints added in 2.5 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 75.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 23 Processing helix chain 'A' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 removed outlier: 3.708A pdb=" N SER A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 149 through 177 Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 removed outlier: 3.785A pdb=" N GLY G 8 " --> pdb=" O TRP G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 23 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.762A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.534A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 110 removed outlier: 3.708A pdb=" N SER G 86 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 149 through 177 Processing helix chain 'G' and resid 204 through 238 removed outlier: 3.625A pdb=" N GLU G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY B 8 " --> pdb=" O TRP B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 23 Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.590A pdb=" N PHE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 removed outlier: 3.708A pdb=" N SER B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 149 through 177 Processing helix chain 'B' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY C 8 " --> pdb=" O TRP C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 23 Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.760A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 149 through 177 Processing helix chain 'C' and resid 204 through 238 removed outlier: 3.627A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY D 8 " --> pdb=" O TRP D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 23 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.590A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 149 through 177 Processing helix chain 'D' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.785A pdb=" N GLY E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 23 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 149 through 177 Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY F 8 " --> pdb=" O TRP F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 23 Processing helix chain 'F' and resid 24 through 40 removed outlier: 3.590A pdb=" N PHE F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 removed outlier: 3.708A pdb=" N SER F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 149 through 177 Processing helix chain 'F' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY H 8 " --> pdb=" O TRP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 23 Processing helix chain 'H' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 45' Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER H 86 " --> pdb=" O ILE H 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 87 " --> pdb=" O ILE H 83 " (cutoff:3.500A) Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 149 through 177 Processing helix chain 'H' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY I 8 " --> pdb=" O TRP I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 23 Processing helix chain 'I' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 45' Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER I 86 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 87 " --> pdb=" O ILE I 83 " (cutoff:3.500A) Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 149 through 177 Processing helix chain 'I' and resid 204 through 238 removed outlier: 3.625A pdb=" N GLU I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY J 8 " --> pdb=" O TRP J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 23 Processing helix chain 'J' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 87 " --> pdb=" O ILE J 83 " (cutoff:3.500A) Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 149 through 177 Processing helix chain 'J' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY K 8 " --> pdb=" O TRP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 23 Processing helix chain 'K' and resid 24 through 40 removed outlier: 3.589A pdb=" N PHE K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE K 31 " --> pdb=" O SER K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 45' Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 110 removed outlier: 3.707A pdb=" N SER K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL K 87 " --> pdb=" O ILE K 83 " (cutoff:3.500A) Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 149 through 177 Processing helix chain 'K' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 removed outlier: 3.784A pdb=" N GLY L 8 " --> pdb=" O TRP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 Processing helix chain 'L' and resid 24 through 40 removed outlier: 3.590A pdb=" N PHE L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE L 31 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.761A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 45' Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.533A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 110 removed outlier: 3.708A pdb=" N SER L 86 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 149 through 177 Processing helix chain 'L' and resid 204 through 238 removed outlier: 3.626A pdb=" N GLU L 227 " --> pdb=" O LEU L 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1380 hydrogen bonds defined for protein. 4032 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: 12.12 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20040 1.03 - 1.23: 60 1.23 - 1.42: 8844 1.42 - 1.62: 14208 1.62 - 1.81: 144 Bond restraints: 43296 Sorted by residual: bond pdb=" C8 PTY G 408 " pdb=" O7 PTY G 408 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C8 PTY K 414 " pdb=" O7 PTY K 414 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C8 PTY C 413 " pdb=" O7 PTY C 413 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C8 PTY D 415 " pdb=" O7 PTY D 415 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C8 PTY J 414 " pdb=" O7 PTY J 414 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 43291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 75376 3.41 - 6.82: 896 6.82 - 10.23: 24 10.23 - 13.65: 12 13.65 - 17.06: 12 Bond angle restraints: 76320 Sorted by residual: angle pdb=" O11 PTY A 408 " pdb=" P1 PTY A 408 " pdb=" O14 PTY A 408 " ideal model delta sigma weight residual 92.90 109.96 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O11 PTY H 414 " pdb=" P1 PTY H 414 " pdb=" O14 PTY H 414 " ideal model delta sigma weight residual 92.90 109.95 -17.05 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O11 PTY K 414 " pdb=" P1 PTY K 414 " pdb=" O14 PTY K 414 " ideal model delta sigma weight residual 92.90 109.94 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O11 PTY F 401 " pdb=" P1 PTY F 401 " pdb=" O14 PTY F 401 " ideal model delta sigma weight residual 92.90 109.94 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O11 PTY I 414 " pdb=" P1 PTY I 414 " pdb=" O14 PTY I 414 " ideal model delta sigma weight residual 92.90 109.94 -17.04 3.00e+00 1.11e-01 3.23e+01 ... (remaining 76315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 21218 29.92 - 59.84: 1030 59.84 - 89.75: 60 89.75 - 119.67: 60 119.67 - 149.59: 12 Dihedral angle restraints: 22380 sinusoidal: 13368 harmonic: 9012 Sorted by residual: dihedral pdb=" C3 PTY G 408 " pdb=" O11 PTY G 408 " pdb=" P1 PTY G 408 " pdb=" O12 PTY G 408 " ideal model delta sinusoidal sigma weight residual 300.23 150.64 149.59 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C3 PTY J 414 " pdb=" O11 PTY J 414 " pdb=" P1 PTY J 414 " pdb=" O12 PTY J 414 " ideal model delta sinusoidal sigma weight residual 300.23 150.65 149.58 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C3 PTY A 408 " pdb=" O11 PTY A 408 " pdb=" P1 PTY A 408 " pdb=" O12 PTY A 408 " ideal model delta sinusoidal sigma weight residual 300.23 150.67 149.56 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 22377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2143 0.031 - 0.062: 784 0.062 - 0.093: 302 0.093 - 0.123: 59 0.123 - 0.154: 24 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CBC Y01 K 413 " pdb=" CAR Y01 K 413 " pdb=" CAV Y01 K 413 " pdb=" OAW Y01 K 413 " both_signs ideal model delta sigma weight residual False -2.54 -2.39 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CBC Y01 E 413 " pdb=" CAR Y01 E 413 " pdb=" CAV Y01 E 413 " pdb=" OAW Y01 E 413 " both_signs ideal model delta sigma weight residual False -2.54 -2.39 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CBC Y01 F 414 " pdb=" CAR Y01 F 414 " pdb=" CAV Y01 F 414 " pdb=" OAW Y01 F 414 " both_signs ideal model delta sigma weight residual False -2.54 -2.39 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 3309 not shown) Planarity restraints: 5724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS G 192 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO G 193 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 193 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS J 192 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO J 193 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO J 193 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO J 193 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 192 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.45e+00 pdb=" N PRO A 193 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.017 5.00e-02 4.00e+02 ... (remaining 5721 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 3808 2.25 - 2.84: 87635 2.84 - 3.43: 95028 3.43 - 4.01: 132350 4.01 - 4.60: 213604 Nonbonded interactions: 532425 Sorted by model distance: nonbonded pdb=" O ILE C 72 " pdb=" HH TYR C 177 " model vdw 1.665 2.450 nonbonded pdb=" O ILE K 72 " pdb=" HH TYR K 177 " model vdw 1.666 2.450 nonbonded pdb=" O ILE F 72 " pdb=" HH TYR F 177 " model vdw 1.666 2.450 nonbonded pdb=" O ILE B 72 " pdb=" HH TYR B 177 " model vdw 1.666 2.450 nonbonded pdb=" O ILE A 72 " pdb=" HH TYR A 177 " model vdw 1.666 2.450 ... (remaining 532420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 238 or resid 402 through 403 or (resid 404 throu \ gh 405 and (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14)) or resid 409 through 410)) selection = (chain 'B' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'C' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'D' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'E' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'F' and (resid 2 through 238 or resid 402 through 403 or (resid 404 throu \ gh 405 and (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14)) or resid 409 through 410)) selection = (chain 'G' and (resid 2 through 238 or resid 402 through 403 or (resid 404 throu \ gh 405 and (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14)) or resid 409 through 410)) selection = (chain 'H' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'I' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'J' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'K' and (resid 2 through 238 or resid 402 through 404 or (resid 405 and ( \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09 or name C10 or name C11 or name C12 or name C13 or name C14)) or re \ sid 409 through 410)) selection = (chain 'L' and (resid 2 through 238 or resid 402 through 403 or (resid 404 throu \ gh 405 and (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14)) or resid 409 through 410)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.540 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 68.040 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.006 0.068 23256 Z= 0.356 Angle : 1.122 17.056 30816 Z= 0.421 Chirality : 0.038 0.154 3312 Planarity : 0.004 0.030 3396 Dihedral : 18.745 149.591 10632 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.10 % Allowed : 3.04 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2376 helix: 2.62 (0.12), residues: 1644 sheet: 1.37 (0.55), residues: 132 loop : -2.01 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 45 HIS 0.005 0.001 HIS A 194 PHE 0.009 0.001 PHE I 97 TYR 0.010 0.001 TYR C 177 ARG 0.002 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 2.331 Fit side-chains REVERT: G 9 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7258 (mttp) REVERT: G 93 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6866 (tt) REVERT: B 9 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7188 (mmtp) REVERT: B 93 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7205 (tt) REVERT: C 9 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7335 (mttp) REVERT: C 93 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6836 (tt) REVERT: D 9 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7267 (mttp) REVERT: D 93 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6989 (tt) REVERT: E 9 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7213 (mmtp) REVERT: F 9 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7174 (mmtp) REVERT: H 93 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6945 (tt) REVERT: I 9 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7258 (mmtp) REVERT: I 93 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7107 (tt) REVERT: J 9 LYS cc_start: 0.7580 (mtpp) cc_final: 0.7149 (mmtp) REVERT: J 188 LYS cc_start: 0.8742 (tttp) cc_final: 0.8488 (tttt) REVERT: K 9 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7237 (mttp) REVERT: K 93 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7057 (tt) REVERT: L 9 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7281 (mmtp) REVERT: L 93 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7142 (tt) outliers start: 24 outliers final: 2 residues processed: 231 average time/residue: 1.8713 time to fit residues: 505.7964 Evaluate side-chains 165 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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: 0.8542 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 23256 Z= 0.161 Angle : 0.602 7.098 30816 Z= 0.291 Chirality : 0.034 0.116 3312 Planarity : 0.004 0.037 3396 Dihedral : 18.765 146.149 6068 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.64 % Allowed : 6.03 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2376 helix: 2.48 (0.12), residues: 1668 sheet: 0.28 (0.39), residues: 204 loop : -1.90 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 45 HIS 0.005 0.002 HIS J 194 PHE 0.009 0.001 PHE E 97 TYR 0.008 0.001 TYR D 230 ARG 0.002 0.000 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 2.383 Fit side-chains REVERT: A 47 ASP cc_start: 0.8858 (p0) cc_final: 0.8608 (p0) REVERT: G 9 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7282 (mttp) REVERT: G 47 ASP cc_start: 0.8851 (p0) cc_final: 0.8577 (p0) REVERT: G 93 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7205 (tt) REVERT: B 9 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7269 (mttp) REVERT: B 93 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7248 (tt) REVERT: C 9 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7330 (mttp) REVERT: C 93 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7110 (tt) REVERT: D 93 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7222 (tt) REVERT: E 9 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7289 (mmtp) REVERT: F 9 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7299 (mmtp) REVERT: I 9 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7291 (mmtp) REVERT: I 93 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7193 (tt) REVERT: J 9 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7231 (mmtp) REVERT: K 93 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7180 (tt) REVERT: L 9 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7292 (mmtp) REVERT: L 47 ASP cc_start: 0.8716 (p0) cc_final: 0.8454 (p0) REVERT: L 93 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7263 (tt) REVERT: L 188 LYS cc_start: 0.8881 (tttp) cc_final: 0.8626 (tttt) outliers start: 14 outliers final: 2 residues processed: 208 average time/residue: 1.8179 time to fit residues: 445.6150 Evaluate side-chains 195 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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: 0.8587 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23256 Z= 0.172 Angle : 0.555 5.794 30816 Z= 0.271 Chirality : 0.034 0.120 3312 Planarity : 0.004 0.039 3396 Dihedral : 15.719 114.662 6066 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.92 % Allowed : 7.73 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.18), residues: 2376 helix: 2.64 (0.12), residues: 1680 sheet: -0.26 (0.38), residues: 204 loop : -1.83 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 45 HIS 0.006 0.001 HIS J 194 PHE 0.009 0.001 PHE E 97 TYR 0.007 0.001 TYR D 155 ARG 0.002 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 2.350 Fit side-chains REVERT: G 9 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7249 (mttp) REVERT: G 93 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7307 (tt) REVERT: B 9 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7280 (mttp) REVERT: B 93 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7373 (tt) REVERT: C 9 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7292 (mttp) REVERT: C 93 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7273 (tt) REVERT: D 9 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7292 (mttp) REVERT: D 190 ASP cc_start: 0.7629 (m-30) cc_final: 0.7387 (m-30) REVERT: D 229 PHE cc_start: 0.6863 (m-10) cc_final: 0.6346 (t80) REVERT: E 9 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7256 (mttp) REVERT: F 9 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7295 (mttp) REVERT: I 9 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7271 (mttp) REVERT: I 93 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7320 (tt) REVERT: J 9 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7248 (mttt) REVERT: J 229 PHE cc_start: 0.6888 (m-10) cc_final: 0.6342 (t80) REVERT: K 9 LYS cc_start: 0.7830 (mmmm) cc_final: 0.7285 (mttp) REVERT: K 93 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7390 (tt) REVERT: K 229 PHE cc_start: 0.6846 (m-10) cc_final: 0.6315 (t80) REVERT: L 9 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7282 (mttp) REVERT: L 93 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7389 (tt) outliers start: 20 outliers final: 8 residues processed: 211 average time/residue: 1.9063 time to fit residues: 470.7935 Evaluate side-chains 202 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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: 0.8664 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23256 Z= 0.248 Angle : 0.612 6.682 30816 Z= 0.307 Chirality : 0.036 0.130 3312 Planarity : 0.005 0.046 3396 Dihedral : 15.757 110.590 6066 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.66 % Allowed : 7.87 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.18), residues: 2376 helix: 2.47 (0.12), residues: 1680 sheet: -0.35 (0.38), residues: 204 loop : -1.87 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 45 HIS 0.008 0.002 HIS D 194 PHE 0.012 0.002 PHE E 97 TYR 0.008 0.002 TYR F 98 ARG 0.003 0.000 ARG H 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 2.373 Fit side-chains REVERT: A 93 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7622 (tt) REVERT: G 9 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7309 (mttp) REVERT: G 93 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (tt) REVERT: G 213 MET cc_start: 0.8923 (mmm) cc_final: 0.8707 (mmm) REVERT: B 93 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7605 (tt) REVERT: C 9 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7356 (mmtp) REVERT: C 93 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7451 (tt) REVERT: D 93 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7563 (tt) REVERT: D 229 PHE cc_start: 0.6825 (m-10) cc_final: 0.6290 (t80) REVERT: E 9 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7359 (mttp) REVERT: F 9 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7358 (mttp) REVERT: H 93 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7533 (tt) REVERT: I 93 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7557 (tt) REVERT: J 9 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7288 (mttp) REVERT: J 229 PHE cc_start: 0.6844 (m-10) cc_final: 0.6338 (t80) REVERT: K 93 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7545 (tt) REVERT: K 229 PHE cc_start: 0.6846 (m-10) cc_final: 0.6297 (t80) REVERT: L 93 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7575 (tt) outliers start: 36 outliers final: 11 residues processed: 252 average time/residue: 2.1336 time to fit residues: 618.0154 Evaluate side-chains 225 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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: 0.8671 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23256 Z= 0.246 Angle : 0.617 7.690 30816 Z= 0.310 Chirality : 0.036 0.127 3312 Planarity : 0.005 0.043 3396 Dihedral : 15.596 106.526 6066 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.38 % Allowed : 9.76 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.99 (0.18), residues: 2376 helix: 2.40 (0.12), residues: 1680 sheet: -0.45 (0.37), residues: 204 loop : -1.86 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 45 HIS 0.007 0.002 HIS A 194 PHE 0.011 0.002 PHE E 97 TYR 0.008 0.002 TYR H 230 ARG 0.002 0.000 ARG I 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 2.361 Fit side-chains REVERT: A 93 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7566 (tt) REVERT: G 9 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7337 (mttt) REVERT: G 93 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (tt) REVERT: G 105 LYS cc_start: 0.6877 (ttpp) cc_final: 0.6632 (ttmp) REVERT: B 9 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7278 (mttp) REVERT: B 93 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7635 (tt) REVERT: C 9 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7360 (mmtp) REVERT: C 93 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7472 (tt) REVERT: D 93 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7589 (tt) REVERT: D 229 PHE cc_start: 0.6804 (m-10) cc_final: 0.6292 (t80) REVERT: E 9 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7347 (mttp) REVERT: F 9 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7378 (mttp) REVERT: F 12 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: H 12 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: H 93 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7574 (tt) REVERT: I 9 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7266 (mmtp) REVERT: I 93 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7608 (tt) REVERT: J 9 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7264 (mttp) REVERT: J 229 PHE cc_start: 0.6857 (m-10) cc_final: 0.6347 (t80) REVERT: K 93 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7584 (tt) REVERT: K 229 PHE cc_start: 0.6816 (m-10) cc_final: 0.6294 (t80) REVERT: L 9 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7292 (mttp) REVERT: L 93 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7634 (tt) outliers start: 30 outliers final: 10 residues processed: 223 average time/residue: 2.0324 time to fit residues: 525.4939 Evaluate side-chains 216 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.8625 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 23256 Z= 0.158 Angle : 0.547 6.604 30816 Z= 0.273 Chirality : 0.033 0.113 3312 Planarity : 0.004 0.040 3396 Dihedral : 14.722 98.507 6066 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.24 % Allowed : 9.99 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2376 helix: 2.74 (0.12), residues: 1668 sheet: -0.38 (0.39), residues: 204 loop : -2.04 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 45 HIS 0.004 0.001 HIS K 194 PHE 0.007 0.001 PHE E 97 TYR 0.005 0.001 TYR A 230 ARG 0.001 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 2.372 Fit side-chains REVERT: A 93 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7564 (tt) REVERT: G 9 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7301 (mttt) REVERT: G 93 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7433 (tt) REVERT: B 9 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7269 (mttp) REVERT: B 93 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7572 (tt) REVERT: C 9 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7310 (mmtp) REVERT: C 93 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7415 (tt) REVERT: D 93 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7568 (tt) REVERT: E 9 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7315 (mttp) REVERT: F 9 LYS cc_start: 0.7772 (mtpp) cc_final: 0.7310 (mttp) REVERT: H 93 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7521 (tt) REVERT: I 9 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7245 (mmtp) REVERT: I 93 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7538 (tt) REVERT: J 9 LYS cc_start: 0.7707 (mtpp) cc_final: 0.7237 (mttp) REVERT: K 93 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7563 (tt) REVERT: L 9 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7292 (mttp) REVERT: L 93 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7569 (tt) outliers start: 27 outliers final: 9 residues processed: 219 average time/residue: 1.9368 time to fit residues: 494.6634 Evaluate side-chains 210 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8695 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23256 Z= 0.305 Angle : 0.657 7.477 30816 Z= 0.331 Chirality : 0.037 0.136 3312 Planarity : 0.005 0.041 3396 Dihedral : 15.446 95.051 6066 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.52 % Allowed : 10.50 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.87 (0.17), residues: 2376 helix: 2.38 (0.12), residues: 1668 sheet: -0.66 (0.35), residues: 204 loop : -2.01 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 45 HIS 0.007 0.002 HIS A 194 PHE 0.012 0.002 PHE E 97 TYR 0.009 0.002 TYR L 98 ARG 0.003 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 2.398 Fit side-chains REVERT: A 93 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7644 (tt) REVERT: G 9 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7390 (mttt) REVERT: G 93 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7595 (tt) REVERT: B 9 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7334 (mttp) REVERT: B 93 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7710 (tt) REVERT: C 9 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7399 (mttt) REVERT: C 93 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7583 (tt) REVERT: D 12 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: D 93 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7630 (tt) REVERT: F 9 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7403 (mttp) REVERT: H 12 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: H 93 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7597 (tt) REVERT: I 9 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7318 (mmtp) REVERT: I 93 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7690 (tt) REVERT: J 9 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7370 (mttp) REVERT: K 12 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: K 93 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7598 (tt) REVERT: L 9 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7374 (mttp) REVERT: L 93 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7704 (tt) outliers start: 33 outliers final: 7 residues processed: 214 average time/residue: 1.9345 time to fit residues: 482.8617 Evaluate side-chains 204 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8680 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23256 Z= 0.245 Angle : 0.610 7.324 30816 Z= 0.307 Chirality : 0.036 0.126 3312 Planarity : 0.005 0.039 3396 Dihedral : 15.192 95.029 6066 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.87 % Allowed : 10.91 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.88 (0.17), residues: 2376 helix: 2.40 (0.12), residues: 1668 sheet: -0.66 (0.36), residues: 204 loop : -2.02 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 45 HIS 0.006 0.002 HIS L 194 PHE 0.009 0.002 PHE L 97 TYR 0.007 0.001 TYR B 98 ARG 0.002 0.000 ARG G 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 2.396 Fit side-chains REVERT: A 93 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7616 (tt) REVERT: G 9 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7396 (mttt) REVERT: G 93 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7588 (tt) REVERT: B 9 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7341 (mttp) REVERT: B 93 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7706 (tt) REVERT: C 9 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7395 (mttt) REVERT: C 93 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7582 (tt) REVERT: D 12 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: D 93 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7579 (tt) REVERT: E 9 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7350 (mttp) REVERT: F 9 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7403 (mttp) REVERT: H 93 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7563 (tt) REVERT: I 9 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7309 (mmtp) REVERT: I 93 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7667 (tt) REVERT: J 9 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7387 (mttp) REVERT: K 12 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: K 93 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7565 (tt) REVERT: L 9 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7361 (mttp) REVERT: L 93 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7701 (tt) outliers start: 19 outliers final: 8 residues processed: 204 average time/residue: 2.0195 time to fit residues: 478.4146 Evaluate side-chains 206 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8668 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23256 Z= 0.217 Angle : 0.588 7.126 30816 Z= 0.296 Chirality : 0.035 0.121 3312 Planarity : 0.005 0.039 3396 Dihedral : 14.795 95.082 6066 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.92 % Allowed : 10.91 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2376 helix: 2.51 (0.12), residues: 1668 sheet: -0.67 (0.36), residues: 204 loop : -2.03 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 45 HIS 0.006 0.002 HIS C 194 PHE 0.009 0.001 PHE H 52 TYR 0.007 0.001 TYR E 98 ARG 0.002 0.000 ARG G 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 2.391 Fit side-chains REVERT: A 93 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7585 (tt) REVERT: G 9 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7393 (mttt) REVERT: G 93 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 9 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7355 (mttp) REVERT: B 93 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7705 (tt) REVERT: C 9 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7386 (mttt) REVERT: C 93 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7582 (tt) REVERT: D 93 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7569 (tt) REVERT: E 9 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7333 (mttp) REVERT: F 9 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7396 (mttp) REVERT: H 12 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: H 93 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7542 (tt) REVERT: I 9 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7303 (mmtp) REVERT: I 93 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7665 (tt) REVERT: J 9 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7389 (mttp) REVERT: K 93 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (tt) REVERT: L 9 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7348 (mttp) REVERT: L 93 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7700 (tt) outliers start: 20 outliers final: 9 residues processed: 202 average time/residue: 2.0084 time to fit residues: 471.0239 Evaluate side-chains 200 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.8656 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23256 Z= 0.200 Angle : 0.573 6.919 30816 Z= 0.288 Chirality : 0.034 0.119 3312 Planarity : 0.005 0.039 3396 Dihedral : 14.403 94.353 6066 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.97 % Allowed : 11.05 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2376 helix: 2.61 (0.12), residues: 1668 sheet: -0.60 (0.37), residues: 204 loop : -2.06 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 45 HIS 0.005 0.001 HIS D 194 PHE 0.008 0.001 PHE L 97 TYR 0.006 0.001 TYR D 98 ARG 0.001 0.000 ARG G 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 2.432 Fit side-chains REVERT: A 93 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7587 (tt) REVERT: G 9 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7363 (mttt) REVERT: G 93 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 9 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7327 (mttt) REVERT: B 93 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7710 (tt) REVERT: D 93 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7566 (tt) REVERT: E 9 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7333 (mttp) REVERT: F 9 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7391 (mttp) REVERT: H 93 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7553 (tt) REVERT: I 9 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7301 (mmtp) REVERT: I 93 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7669 (tt) REVERT: J 9 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7343 (mttp) REVERT: K 93 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7538 (tt) REVERT: L 9 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7339 (mttp) REVERT: L 93 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7701 (tt) outliers start: 21 outliers final: 9 residues processed: 196 average time/residue: 2.0655 time to fit residues: 472.1153 Evaluate side-chains 194 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.149995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102986 restraints weight = 59398.455| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.08 r_work: 0.2835 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23256 Z= 0.231 Angle : 0.594 7.005 30816 Z= 0.298 Chirality : 0.035 0.123 3312 Planarity : 0.005 0.039 3396 Dihedral : 14.419 94.893 6064 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.87 % Allowed : 11.14 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2376 helix: 2.54 (0.12), residues: 1668 sheet: -0.67 (0.36), residues: 204 loop : -2.02 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.005 0.001 HIS D 194 PHE 0.009 0.002 PHE H 52 TYR 0.007 0.001 TYR K 98 ARG 0.001 0.000 ARG G 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8776.83 seconds wall clock time: 151 minutes 26.57 seconds (9086.57 seconds total)