Starting phenix.real_space_refine on Fri Dec 27 13:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqd_33393/12_2024/7xqd_33393_trim.cif" } resolution = 2.7 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= 0.003 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 24 5.49 5 S 96 5.16 5 C 15852 2.51 5 N 3144 2.21 5 O 3896 1.98 5 H 19968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42980 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "G" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "H" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "I" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "J" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "L" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3300 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "D" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "E" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "G" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "H" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "I" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "J" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "K" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "L" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'C14': 9, 'PTY': 2, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 15.98, per 1000 atoms: 0.37 Number of scatterers: 42980 At special positions: 0 Unit cell: (107.696, 111.936, 181.472, 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 24 15.00 O 3896 8.00 N 3144 7.00 C 15852 6.00 H 19968 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 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 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 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: 8.39 Conformation dependent library (CDL) restraints added in 2.3 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.529A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 177 Processing helix chain 'A' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.875A pdb=" N LYS B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 177 Processing helix chain 'B' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 177 Processing helix chain 'C' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 19 through 40 removed outlier: 3.875A pdb=" N LYS D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.531A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 177 Processing helix chain 'D' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 177 Processing helix chain 'E' and resid 202 through 237 removed outlier: 4.144A pdb=" N LYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 177 Processing helix chain 'F' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'G' and resid 73 through 110 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 151 through 177 Processing helix chain 'G' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS G 237 " --> pdb=" O PHE G 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.799A 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 Processing helix chain 'H' and resid 73 through 110 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 151 through 177 Processing helix chain 'H' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS H 237 " --> pdb=" O PHE H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'I' and resid 73 through 110 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 151 through 177 Processing helix chain 'I' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS I 237 " --> pdb=" O PHE I 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.531A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'J' and resid 73 through 110 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 151 through 177 Processing helix chain 'J' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS J 237 " --> pdb=" O PHE J 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.531A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'K' and resid 73 through 110 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 151 through 177 Processing helix chain 'K' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS K 237 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.876A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.530A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.800A 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 Processing helix chain 'L' and resid 73 through 110 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 151 through 177 Processing helix chain 'L' and resid 202 through 237 removed outlier: 4.145A pdb=" N LYS L 237 " --> pdb=" O PHE L 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.533A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.533A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.532A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4284 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: 11.51 Time building geometry restraints manager: 10.14 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: 19968 1.03 - 1.23: 72 1.23 - 1.42: 8880 1.42 - 1.61: 14076 1.61 - 1.81: 168 Bond restraints: 43164 Sorted by residual: bond pdb=" C8 PTY A 308 " pdb=" O7 PTY A 308 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C8 PTY I 313 " pdb=" O7 PTY I 313 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C8 PTY F 301 " pdb=" O7 PTY F 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C30 PTY D 310 " pdb=" O4 PTY D 310 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C8 PTY G 308 " pdb=" O7 PTY G 308 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 43159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 74960 3.35 - 6.71: 1072 6.71 - 10.06: 48 10.06 - 13.42: 24 13.42 - 16.77: 24 Bond angle restraints: 76128 Sorted by residual: angle pdb=" O11 PTY H 310 " pdb=" P1 PTY H 310 " pdb=" O14 PTY H 310 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY E 310 " pdb=" P1 PTY E 310 " pdb=" O14 PTY E 310 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY F 311 " pdb=" P1 PTY F 311 " pdb=" O14 PTY F 311 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY A 305 " pdb=" P1 PTY A 305 " pdb=" O14 PTY A 305 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY D 310 " pdb=" P1 PTY D 310 " pdb=" O14 PTY D 310 " ideal model delta sigma weight residual 92.90 109.66 -16.76 3.00e+00 1.11e-01 3.12e+01 ... (remaining 76123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 20986 24.91 - 49.83: 962 49.83 - 74.74: 240 74.74 - 99.65: 84 99.65 - 124.56: 36 Dihedral angle restraints: 22308 sinusoidal: 13332 harmonic: 8976 Sorted by residual: dihedral pdb=" N1 PTY F 311 " pdb=" C2 PTY F 311 " pdb=" C3 PTY F 311 " pdb=" O11 PTY F 311 " ideal model delta sinusoidal sigma weight residual 65.33 -170.11 -124.56 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" N1 PTY H 310 " pdb=" C2 PTY H 310 " pdb=" C3 PTY H 310 " pdb=" O11 PTY H 310 " ideal model delta sinusoidal sigma weight residual 65.33 -170.13 -124.54 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" N1 PTY G 305 " pdb=" C2 PTY G 305 " pdb=" C3 PTY G 305 " pdb=" O11 PTY G 305 " ideal model delta sinusoidal sigma weight residual 65.33 -170.14 -124.53 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 22305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2340 0.033 - 0.065: 640 0.065 - 0.098: 250 0.098 - 0.131: 58 0.131 - 0.163: 24 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CBC Y01 J 312 " pdb=" CAR Y01 J 312 " pdb=" CAV Y01 J 312 " pdb=" OAW Y01 J 312 " both_signs ideal model delta sigma weight residual False -2.54 -2.38 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CBC Y01 A 307 " pdb=" CAR Y01 A 307 " pdb=" CAV Y01 A 307 " pdb=" OAW Y01 A 307 " both_signs ideal model delta sigma weight residual False -2.54 -2.38 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CBC Y01 E 312 " pdb=" CAR Y01 E 312 " pdb=" CAV Y01 E 312 " pdb=" OAW Y01 E 312 " both_signs ideal model delta sigma weight residual False -2.54 -2.38 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 3309 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 202 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO H 203 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO H 203 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 203 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 202 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.06e-01 pdb=" N PRO G 203 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO G 203 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 203 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 202 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.03e-01 pdb=" N PRO L 203 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 203 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 203 " -0.013 5.00e-02 4.00e+02 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 2157 2.22 - 2.81: 82641 2.81 - 3.41: 106009 3.41 - 4.00: 137136 4.00 - 4.60: 223765 Nonbonded interactions: 551708 Sorted by model distance: nonbonded pdb=" OE1 GLU A 111 " pdb=" H GLU A 111 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU L 111 " pdb=" H GLU L 111 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU J 111 " pdb=" H GLU J 111 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU K 111 " pdb=" H GLU K 111 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU D 111 " pdb=" H GLU D 111 " model vdw 1.619 2.450 ... (remaining 551703 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 302 through 303 or (resid 304 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 309)) selection = (chain 'B' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'C' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'D' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'E' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'F' and (resid 2 through 238 or resid 302 through 303 or (resid 304 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 309)) selection = (chain 'G' and (resid 2 through 238 or resid 302 through 303 or (resid 304 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 309)) selection = (chain 'H' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'I' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'J' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'K' and (resid 2 through 238 or resid 302 through 304 or resid 309)) selection = (chain 'L' and (resid 2 through 238 or resid 302 through 303 or (resid 304 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 309)) } 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: 1.180 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: 0.560 Extract box with map and model: 1.190 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 63.330 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 0.069 23196 Z= 0.347 Angle : 1.174 16.774 30804 Z= 0.424 Chirality : 0.038 0.163 3312 Planarity : 0.003 0.024 3396 Dihedral : 17.825 124.563 10596 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.56 % Allowed : 1.11 % Favored : 98.33 % 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: 3.53 (0.17), residues: 2364 helix: 3.29 (0.12), residues: 1716 sheet: 2.75 (0.42), residues: 120 loop : -1.31 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 78 HIS 0.001 0.001 HIS G 194 PHE 0.008 0.001 PHE D 32 TYR 0.008 0.001 TYR H 155 ARG 0.001 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 500 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8197 (m100) cc_final: 0.7911 (m-10) REVERT: A 12 ASP cc_start: 0.8614 (m-30) cc_final: 0.7950 (m-30) REVERT: A 234 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8096 (tppt) REVERT: B 4 TRP cc_start: 0.8043 (m100) cc_final: 0.7798 (m-10) REVERT: B 12 ASP cc_start: 0.8889 (m-30) cc_final: 0.8521 (m-30) REVERT: C 4 TRP cc_start: 0.8052 (m100) cc_final: 0.7769 (m100) REVERT: C 5 SER cc_start: 0.7701 (m) cc_final: 0.7435 (p) REVERT: C 36 LEU cc_start: 0.8850 (tp) cc_final: 0.8557 (tp) REVERT: C 103 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 233 PHE cc_start: 0.8107 (t80) cc_final: 0.7764 (t80) REVERT: D 4 TRP cc_start: 0.8195 (m100) cc_final: 0.7822 (m-10) REVERT: E 4 TRP cc_start: 0.8059 (m100) cc_final: 0.7840 (m-10) REVERT: E 12 ASP cc_start: 0.8695 (m-30) cc_final: 0.8441 (m-30) REVERT: E 233 PHE cc_start: 0.7998 (t80) cc_final: 0.7787 (t80) REVERT: F 101 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8021 (mtp180) REVERT: G 4 TRP cc_start: 0.8384 (m100) cc_final: 0.7640 (m-90) REVERT: G 12 ASP cc_start: 0.8659 (m-30) cc_final: 0.8170 (m-30) REVERT: H 4 TRP cc_start: 0.8152 (m100) cc_final: 0.7634 (m-10) REVERT: H 174 TRP cc_start: 0.8402 (t60) cc_final: 0.7970 (t60) REVERT: I 233 PHE cc_start: 0.7674 (t80) cc_final: 0.7406 (t80) REVERT: J 4 TRP cc_start: 0.7882 (m100) cc_final: 0.7662 (m-10) REVERT: J 104 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7252 (mp0) REVERT: J 230 TYR cc_start: 0.8591 (t80) cc_final: 0.8347 (t80) REVERT: J 233 PHE cc_start: 0.8185 (t80) cc_final: 0.7813 (t80) REVERT: K 12 ASP cc_start: 0.8516 (m-30) cc_final: 0.8094 (m-30) REVERT: L 4 TRP cc_start: 0.7947 (m100) cc_final: 0.7582 (m-10) outliers start: 12 outliers final: 0 residues processed: 504 average time/residue: 2.3008 time to fit residues: 1322.0353 Evaluate side-chains 339 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8741 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23196 Z= 0.249 Angle : 0.665 7.803 30804 Z= 0.311 Chirality : 0.037 0.144 3312 Planarity : 0.004 0.061 3396 Dihedral : 17.085 109.153 6048 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.78 % Allowed : 11.25 % Favored : 85.97 % 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: 3.35 (0.17), residues: 2364 helix: 3.17 (0.12), residues: 1704 sheet: 2.73 (0.42), residues: 120 loop : -1.34 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 25 HIS 0.003 0.001 HIS F 194 PHE 0.012 0.002 PHE F 32 TYR 0.010 0.002 TYR A 66 ARG 0.007 0.001 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 347 time to evaluate : 2.457 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8146 (m100) cc_final: 0.7785 (m-10) REVERT: A 12 ASP cc_start: 0.8597 (m-30) cc_final: 0.8100 (m-30) REVERT: A 42 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 89 THR cc_start: 0.8380 (m) cc_final: 0.8049 (m) REVERT: A 234 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8087 (tppt) REVERT: B 4 TRP cc_start: 0.8101 (m100) cc_final: 0.7755 (m-10) REVERT: B 12 ASP cc_start: 0.8894 (m-30) cc_final: 0.8551 (m-30) REVERT: B 42 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: C 4 TRP cc_start: 0.7987 (m100) cc_final: 0.7770 (m100) REVERT: C 9 LYS cc_start: 0.9099 (mttt) cc_final: 0.8855 (mttm) REVERT: C 231 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 233 PHE cc_start: 0.8248 (t80) cc_final: 0.7879 (t80) REVERT: D 4 TRP cc_start: 0.8265 (m100) cc_final: 0.7712 (m-10) REVERT: E 4 TRP cc_start: 0.8144 (m100) cc_final: 0.7847 (m-10) REVERT: E 12 ASP cc_start: 0.8649 (m-30) cc_final: 0.8426 (m-30) REVERT: E 42 GLU cc_start: 0.8340 (tt0) cc_final: 0.7543 (tt0) REVERT: E 233 PHE cc_start: 0.8029 (t80) cc_final: 0.7814 (t80) REVERT: F 9 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8598 (mtpt) REVERT: F 12 ASP cc_start: 0.8748 (m-30) cc_final: 0.8208 (m-30) REVERT: G 4 TRP cc_start: 0.8319 (m100) cc_final: 0.7513 (m-90) REVERT: G 9 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8855 (mtmm) REVERT: G 12 ASP cc_start: 0.8657 (m-30) cc_final: 0.8156 (m-30) REVERT: H 4 TRP cc_start: 0.8106 (m100) cc_final: 0.7519 (m-10) REVERT: H 42 GLU cc_start: 0.8323 (tt0) cc_final: 0.7922 (tt0) REVERT: I 4 TRP cc_start: 0.8128 (m100) cc_final: 0.7850 (m100) REVERT: I 233 PHE cc_start: 0.7792 (t80) cc_final: 0.7525 (t80) REVERT: J 4 TRP cc_start: 0.7989 (m100) cc_final: 0.7593 (m-10) REVERT: J 7 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8587 (tt) REVERT: J 42 GLU cc_start: 0.8274 (tt0) cc_final: 0.7641 (tt0) REVERT: J 104 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7396 (mp0) REVERT: J 205 GLU cc_start: 0.8909 (tt0) cc_final: 0.8688 (tt0) REVERT: J 229 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: J 230 TYR cc_start: 0.8606 (t80) cc_final: 0.8309 (t80) REVERT: J 233 PHE cc_start: 0.8274 (t80) cc_final: 0.7919 (t80) REVERT: K 12 ASP cc_start: 0.8559 (m-30) cc_final: 0.8285 (m-30) REVERT: K 42 GLU cc_start: 0.8464 (tt0) cc_final: 0.7979 (tt0) REVERT: L 4 TRP cc_start: 0.7982 (m100) cc_final: 0.7531 (m-10) REVERT: L 33 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8131 (ttm170) outliers start: 60 outliers final: 20 residues processed: 380 average time/residue: 1.9830 time to fit residues: 876.7044 Evaluate side-chains 354 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8721 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23196 Z= 0.149 Angle : 0.532 6.755 30804 Z= 0.253 Chirality : 0.034 0.110 3312 Planarity : 0.003 0.028 3396 Dihedral : 15.008 92.524 6048 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.04 % Allowed : 12.73 % Favored : 85.23 % 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: 3.53 (0.17), residues: 2364 helix: 3.36 (0.12), residues: 1704 sheet: 1.83 (0.45), residues: 132 loop : -1.28 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 25 HIS 0.002 0.000 HIS L 194 PHE 0.011 0.001 PHE B 30 TYR 0.007 0.001 TYR A 66 ARG 0.003 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8138 (m100) cc_final: 0.7791 (m-10) REVERT: A 12 ASP cc_start: 0.8660 (m-30) cc_final: 0.7948 (m-30) REVERT: A 42 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 234 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8066 (tppt) REVERT: B 4 TRP cc_start: 0.8153 (m100) cc_final: 0.7830 (m-10) REVERT: B 12 ASP cc_start: 0.8898 (m-30) cc_final: 0.8568 (m-30) REVERT: B 42 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 9 LYS cc_start: 0.9103 (mttt) cc_final: 0.8837 (mttm) REVERT: C 233 PHE cc_start: 0.8210 (t80) cc_final: 0.7828 (t80) REVERT: D 4 TRP cc_start: 0.8252 (m100) cc_final: 0.7712 (m-10) REVERT: E 4 TRP cc_start: 0.8147 (m100) cc_final: 0.7842 (m-10) REVERT: E 12 ASP cc_start: 0.8616 (m-30) cc_final: 0.8408 (m-30) REVERT: E 233 PHE cc_start: 0.7965 (t80) cc_final: 0.7736 (t80) REVERT: F 12 ASP cc_start: 0.8699 (m-30) cc_final: 0.8241 (m-30) REVERT: G 4 TRP cc_start: 0.8338 (m100) cc_final: 0.7529 (m-90) REVERT: G 12 ASP cc_start: 0.8676 (m-30) cc_final: 0.8189 (m-30) REVERT: H 4 TRP cc_start: 0.8110 (m100) cc_final: 0.7515 (m-10) REVERT: H 42 GLU cc_start: 0.8250 (tt0) cc_final: 0.7862 (tt0) REVERT: H 153 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7770 (ptp90) REVERT: I 4 TRP cc_start: 0.8158 (m100) cc_final: 0.7898 (m100) REVERT: I 233 PHE cc_start: 0.7761 (t80) cc_final: 0.7501 (t80) REVERT: J 4 TRP cc_start: 0.8017 (m100) cc_final: 0.7621 (m-10) REVERT: J 42 GLU cc_start: 0.8306 (tt0) cc_final: 0.7668 (tt0) REVERT: J 229 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: J 230 TYR cc_start: 0.8586 (t80) cc_final: 0.8259 (t80) REVERT: J 233 PHE cc_start: 0.8250 (t80) cc_final: 0.7901 (t80) REVERT: K 12 ASP cc_start: 0.8557 (m-30) cc_final: 0.8266 (m-30) REVERT: K 42 GLU cc_start: 0.8388 (tt0) cc_final: 0.7880 (tt0) REVERT: L 4 TRP cc_start: 0.7992 (m100) cc_final: 0.7533 (m-10) REVERT: L 33 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8133 (ttm170) outliers start: 44 outliers final: 19 residues processed: 364 average time/residue: 2.0274 time to fit residues: 855.9355 Evaluate side-chains 347 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 323 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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: 0.8766 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23196 Z= 0.226 Angle : 0.567 8.393 30804 Z= 0.277 Chirality : 0.035 0.128 3312 Planarity : 0.003 0.042 3396 Dihedral : 14.286 89.381 6048 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.31 % Allowed : 12.41 % Favored : 85.28 % 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: 3.40 (0.17), residues: 2364 helix: 3.25 (0.11), residues: 1704 sheet: 1.82 (0.45), residues: 132 loop : -1.27 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 25 HIS 0.003 0.001 HIS L 194 PHE 0.011 0.001 PHE A 199 TYR 0.020 0.001 TYR J 17 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 2.480 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8156 (m100) cc_final: 0.7746 (m-10) REVERT: A 9 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8930 (mtpt) REVERT: A 12 ASP cc_start: 0.8618 (m-30) cc_final: 0.8177 (m-30) REVERT: A 42 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: A 89 THR cc_start: 0.8310 (m) cc_final: 0.8061 (m) REVERT: A 234 LYS cc_start: 0.8314 (ttpp) cc_final: 0.8075 (tppt) REVERT: B 4 TRP cc_start: 0.8222 (m100) cc_final: 0.7828 (m-10) REVERT: B 12 ASP cc_start: 0.8884 (m-30) cc_final: 0.8546 (m-30) REVERT: B 42 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: C 9 LYS cc_start: 0.9132 (mttt) cc_final: 0.8892 (mttm) REVERT: C 231 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (t) REVERT: C 233 PHE cc_start: 0.8241 (t80) cc_final: 0.7898 (t80) REVERT: E 4 TRP cc_start: 0.8198 (m100) cc_final: 0.7861 (m-10) REVERT: E 12 ASP cc_start: 0.8641 (m-30) cc_final: 0.8426 (m-30) REVERT: E 233 PHE cc_start: 0.7972 (t80) cc_final: 0.7727 (t80) REVERT: F 12 ASP cc_start: 0.8710 (m-30) cc_final: 0.8177 (m-30) REVERT: G 4 TRP cc_start: 0.8293 (m100) cc_final: 0.7459 (m-90) REVERT: G 9 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8914 (mttt) REVERT: G 12 ASP cc_start: 0.8620 (m-30) cc_final: 0.8108 (m-30) REVERT: G 234 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8436 (ttmm) REVERT: H 4 TRP cc_start: 0.8141 (m100) cc_final: 0.7558 (m-10) REVERT: H 42 GLU cc_start: 0.8264 (tt0) cc_final: 0.7887 (tt0) REVERT: I 4 TRP cc_start: 0.8169 (m100) cc_final: 0.7937 (m100) REVERT: I 103 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: I 233 PHE cc_start: 0.7834 (t80) cc_final: 0.7515 (t80) REVERT: J 4 TRP cc_start: 0.8102 (m100) cc_final: 0.7664 (m-10) REVERT: J 42 GLU cc_start: 0.8377 (tt0) cc_final: 0.7782 (tt0) REVERT: J 229 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: J 233 PHE cc_start: 0.8259 (t80) cc_final: 0.7923 (t80) REVERT: K 12 ASP cc_start: 0.8571 (m-30) cc_final: 0.8293 (m-30) REVERT: K 42 GLU cc_start: 0.8512 (tt0) cc_final: 0.8020 (tt0) REVERT: K 104 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8278 (tm-30) REVERT: L 4 TRP cc_start: 0.7993 (m100) cc_final: 0.7521 (m-10) REVERT: L 33 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8257 (ttm170) outliers start: 50 outliers final: 24 residues processed: 345 average time/residue: 2.0109 time to fit residues: 806.3571 Evaluate side-chains 345 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8784 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23196 Z= 0.243 Angle : 0.575 7.991 30804 Z= 0.281 Chirality : 0.035 0.131 3312 Planarity : 0.004 0.036 3396 Dihedral : 13.918 90.113 6048 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.78 % Allowed : 12.92 % Favored : 84.31 % 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: 3.29 (0.17), residues: 2364 helix: 3.16 (0.11), residues: 1704 sheet: 1.74 (0.45), residues: 132 loop : -1.29 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 45 HIS 0.003 0.001 HIS L 194 PHE 0.011 0.002 PHE I 32 TYR 0.010 0.001 TYR A 66 ARG 0.004 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 2.472 Fit side-chains REVERT: A 4 TRP cc_start: 0.8176 (m100) cc_final: 0.7706 (m-10) REVERT: A 42 GLU cc_start: 0.8527 (tt0) cc_final: 0.8085 (tt0) REVERT: A 234 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8059 (tppt) REVERT: B 4 TRP cc_start: 0.8170 (m100) cc_final: 0.7818 (m-10) REVERT: B 12 ASP cc_start: 0.8929 (m-30) cc_final: 0.8592 (m-30) REVERT: B 42 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: C 231 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8254 (t) REVERT: C 233 PHE cc_start: 0.8272 (t80) cc_final: 0.7925 (t80) REVERT: E 4 TRP cc_start: 0.8210 (m100) cc_final: 0.7841 (m-10) REVERT: E 12 ASP cc_start: 0.8682 (m-30) cc_final: 0.8437 (m-30) REVERT: F 12 ASP cc_start: 0.8689 (m-30) cc_final: 0.8143 (m-30) REVERT: G 4 TRP cc_start: 0.8316 (m100) cc_final: 0.7496 (m-90) REVERT: G 12 ASP cc_start: 0.8591 (m-30) cc_final: 0.8055 (m-30) REVERT: G 231 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (t) REVERT: G 234 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8400 (ttmm) REVERT: H 4 TRP cc_start: 0.8240 (m100) cc_final: 0.7589 (m-10) REVERT: H 9 LYS cc_start: 0.9269 (mtmt) cc_final: 0.8887 (ptpp) REVERT: H 42 GLU cc_start: 0.8328 (tt0) cc_final: 0.7899 (tt0) REVERT: I 4 TRP cc_start: 0.8182 (m100) cc_final: 0.7893 (m100) REVERT: I 103 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: I 233 PHE cc_start: 0.7862 (t80) cc_final: 0.7515 (t80) REVERT: J 4 TRP cc_start: 0.8150 (m100) cc_final: 0.7661 (m-10) REVERT: J 42 GLU cc_start: 0.8387 (tt0) cc_final: 0.7871 (tt0) REVERT: J 229 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: J 233 PHE cc_start: 0.8273 (t80) cc_final: 0.7944 (t80) REVERT: K 12 ASP cc_start: 0.8591 (m-30) cc_final: 0.8348 (m-30) REVERT: K 42 GLU cc_start: 0.8469 (tt0) cc_final: 0.8017 (tt0) REVERT: K 104 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8240 (tm-30) REVERT: K 229 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8064 (t80) REVERT: L 4 TRP cc_start: 0.8018 (m100) cc_final: 0.7550 (m-10) REVERT: L 33 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8350 (ttm170) REVERT: L 105 LYS cc_start: 0.8227 (tppt) cc_final: 0.7845 (tttt) outliers start: 60 outliers final: 24 residues processed: 348 average time/residue: 2.0141 time to fit residues: 813.9880 Evaluate side-chains 330 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J 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 227 GLU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.8767 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23196 Z= 0.164 Angle : 0.540 7.710 30804 Z= 0.259 Chirality : 0.034 0.111 3312 Planarity : 0.003 0.030 3396 Dihedral : 13.297 90.064 6048 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.31 % Allowed : 13.61 % Favored : 84.07 % 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: 3.38 (0.17), residues: 2364 helix: 3.25 (0.11), residues: 1704 sheet: 1.71 (0.45), residues: 132 loop : -1.32 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 25 HIS 0.002 0.001 HIS L 194 PHE 0.017 0.001 PHE E 233 TYR 0.016 0.001 TYR J 17 ARG 0.003 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8166 (m100) cc_final: 0.7704 (m-10) REVERT: A 12 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: A 42 GLU cc_start: 0.8536 (tt0) cc_final: 0.8016 (tt0) REVERT: A 234 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8074 (tppt) REVERT: B 4 TRP cc_start: 0.8200 (m100) cc_final: 0.7799 (m-10) REVERT: B 12 ASP cc_start: 0.8897 (m-30) cc_final: 0.8536 (m-30) REVERT: B 42 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: C 231 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (t) REVERT: C 233 PHE cc_start: 0.8278 (t80) cc_final: 0.7935 (t80) REVERT: E 4 TRP cc_start: 0.8245 (m100) cc_final: 0.7842 (m-10) REVERT: E 12 ASP cc_start: 0.8666 (m-30) cc_final: 0.8405 (m-30) REVERT: F 9 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8709 (ptmt) REVERT: F 12 ASP cc_start: 0.8681 (m-30) cc_final: 0.8154 (m-30) REVERT: G 4 TRP cc_start: 0.8309 (m100) cc_final: 0.7613 (m-10) REVERT: G 12 ASP cc_start: 0.8603 (m-30) cc_final: 0.8064 (m-30) REVERT: H 4 TRP cc_start: 0.8242 (m100) cc_final: 0.7584 (m-10) REVERT: H 42 GLU cc_start: 0.8305 (tt0) cc_final: 0.7903 (tt0) REVERT: I 4 TRP cc_start: 0.8212 (m100) cc_final: 0.7934 (m100) REVERT: I 233 PHE cc_start: 0.7813 (t80) cc_final: 0.7476 (t80) REVERT: J 4 TRP cc_start: 0.8197 (m100) cc_final: 0.7705 (m-10) REVERT: J 42 GLU cc_start: 0.8424 (tt0) cc_final: 0.7905 (tt0) REVERT: J 229 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: J 233 PHE cc_start: 0.8258 (t80) cc_final: 0.7931 (t80) REVERT: K 12 ASP cc_start: 0.8557 (m-30) cc_final: 0.8354 (m-30) REVERT: K 42 GLU cc_start: 0.8519 (tt0) cc_final: 0.8076 (tt0) REVERT: K 104 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8219 (tm-30) REVERT: K 229 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8047 (t80) REVERT: L 4 TRP cc_start: 0.8058 (m100) cc_final: 0.7553 (m-10) REVERT: L 33 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8333 (ttm170) REVERT: L 105 LYS cc_start: 0.8242 (tppt) cc_final: 0.7844 (ttmt) outliers start: 50 outliers final: 27 residues processed: 329 average time/residue: 2.0333 time to fit residues: 777.4014 Evaluate side-chains 335 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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: 0.8778 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23196 Z= 0.210 Angle : 0.557 7.581 30804 Z= 0.268 Chirality : 0.035 0.121 3312 Planarity : 0.003 0.043 3396 Dihedral : 13.087 91.673 6048 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.18 % Allowed : 14.35 % Favored : 83.47 % 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: 3.30 (0.17), residues: 2364 helix: 3.14 (0.11), residues: 1716 sheet: 1.69 (0.45), residues: 132 loop : -1.26 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 25 HIS 0.002 0.001 HIS L 194 PHE 0.017 0.001 PHE E 233 TYR 0.015 0.001 TYR J 17 ARG 0.003 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8189 (m100) cc_final: 0.7675 (m-10) REVERT: A 9 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8932 (ptpp) REVERT: A 42 GLU cc_start: 0.8527 (tt0) cc_final: 0.8096 (tt0) REVERT: A 234 LYS cc_start: 0.8318 (ttpp) cc_final: 0.8075 (tppt) REVERT: B 4 TRP cc_start: 0.8239 (m100) cc_final: 0.7793 (m-10) REVERT: B 12 ASP cc_start: 0.8937 (m-30) cc_final: 0.8574 (m-30) REVERT: B 42 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: C 231 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8094 (t) REVERT: C 233 PHE cc_start: 0.8306 (t80) cc_final: 0.7957 (t80) REVERT: D 108 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7881 (tppp) REVERT: E 4 TRP cc_start: 0.8264 (m100) cc_final: 0.7840 (m-10) REVERT: E 12 ASP cc_start: 0.8619 (m-30) cc_final: 0.8367 (m-30) REVERT: F 12 ASP cc_start: 0.8613 (m-30) cc_final: 0.8051 (m-30) REVERT: G 4 TRP cc_start: 0.8319 (m100) cc_final: 0.7568 (m-10) REVERT: G 12 ASP cc_start: 0.8581 (m-30) cc_final: 0.8047 (m-30) REVERT: G 234 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (ttmm) REVERT: H 4 TRP cc_start: 0.8267 (m100) cc_final: 0.7593 (m-10) REVERT: H 9 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8916 (ptpp) REVERT: H 42 GLU cc_start: 0.8327 (tt0) cc_final: 0.7905 (tt0) REVERT: I 4 TRP cc_start: 0.8194 (m100) cc_final: 0.7934 (m100) REVERT: I 103 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: J 4 TRP cc_start: 0.8250 (m100) cc_final: 0.7729 (m-10) REVERT: J 42 GLU cc_start: 0.8402 (tt0) cc_final: 0.7888 (tt0) REVERT: J 229 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: J 233 PHE cc_start: 0.8271 (t80) cc_final: 0.7942 (t80) REVERT: K 12 ASP cc_start: 0.8574 (m-30) cc_final: 0.8359 (m-30) REVERT: K 42 GLU cc_start: 0.8528 (tt0) cc_final: 0.8099 (tt0) REVERT: K 104 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8224 (tm-30) REVERT: K 229 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8056 (t80) REVERT: L 4 TRP cc_start: 0.8030 (m100) cc_final: 0.7501 (m-10) REVERT: L 33 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: L 105 LYS cc_start: 0.8233 (tppt) cc_final: 0.7829 (ttmt) outliers start: 47 outliers final: 28 residues processed: 326 average time/residue: 1.9974 time to fit residues: 756.9633 Evaluate side-chains 329 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8807 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23196 Z= 0.303 Angle : 0.611 7.596 30804 Z= 0.299 Chirality : 0.037 0.136 3312 Planarity : 0.004 0.043 3396 Dihedral : 13.578 95.339 6048 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.73 % Allowed : 14.21 % Favored : 83.06 % 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: 3.00 (0.16), residues: 2364 helix: 3.03 (0.11), residues: 1680 sheet: 1.55 (0.44), residues: 132 loop : -1.49 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 25 HIS 0.003 0.001 HIS L 194 PHE 0.021 0.002 PHE E 233 TYR 0.020 0.002 TYR J 17 ARG 0.003 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 2.473 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8933 (ptpp) REVERT: A 12 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: A 42 GLU cc_start: 0.8502 (tt0) cc_final: 0.8062 (tt0) REVERT: A 234 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8065 (tppt) REVERT: B 4 TRP cc_start: 0.8192 (m100) cc_final: 0.7861 (m-10) REVERT: B 12 ASP cc_start: 0.8920 (m-30) cc_final: 0.8582 (m-30) REVERT: B 42 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: C 231 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8160 (t) REVERT: C 233 PHE cc_start: 0.8332 (t80) cc_final: 0.7990 (t80) REVERT: E 4 TRP cc_start: 0.8258 (m100) cc_final: 0.7817 (m-10) REVERT: E 12 ASP cc_start: 0.8624 (m-30) cc_final: 0.8351 (m-30) REVERT: F 12 ASP cc_start: 0.8578 (m-30) cc_final: 0.8039 (m-30) REVERT: G 4 TRP cc_start: 0.8321 (m100) cc_final: 0.7530 (m-10) REVERT: G 12 ASP cc_start: 0.8587 (m-30) cc_final: 0.8060 (m-30) REVERT: H 4 TRP cc_start: 0.8225 (m100) cc_final: 0.7545 (m-10) REVERT: H 42 GLU cc_start: 0.8376 (tt0) cc_final: 0.7943 (tt0) REVERT: I 4 TRP cc_start: 0.8216 (m100) cc_final: 0.7936 (m100) REVERT: I 103 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: I 233 PHE cc_start: 0.7915 (t80) cc_final: 0.7514 (t80) REVERT: J 4 TRP cc_start: 0.8244 (m100) cc_final: 0.7708 (m-10) REVERT: J 42 GLU cc_start: 0.8397 (tt0) cc_final: 0.7976 (tt0) REVERT: J 229 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: J 233 PHE cc_start: 0.8271 (t80) cc_final: 0.7950 (t80) REVERT: K 42 GLU cc_start: 0.8542 (tt0) cc_final: 0.8186 (tt0) REVERT: K 229 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (t80) REVERT: L 4 TRP cc_start: 0.8056 (m100) cc_final: 0.7581 (m-10) REVERT: L 33 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8361 (ttm170) REVERT: L 105 LYS cc_start: 0.8209 (tppt) cc_final: 0.7808 (ttmt) outliers start: 59 outliers final: 27 residues processed: 323 average time/residue: 2.0149 time to fit residues: 756.7525 Evaluate side-chains 322 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J 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 100 MET Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.8800 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23196 Z= 0.258 Angle : 0.589 7.573 30804 Z= 0.287 Chirality : 0.036 0.193 3312 Planarity : 0.004 0.036 3396 Dihedral : 13.405 96.676 6048 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 15.14 % Favored : 82.78 % 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: 3.00 (0.16), residues: 2364 helix: 3.04 (0.11), residues: 1680 sheet: 1.59 (0.44), residues: 132 loop : -1.53 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 4 HIS 0.002 0.001 HIS L 194 PHE 0.019 0.002 PHE E 233 TYR 0.012 0.001 TYR J 17 ARG 0.003 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8932 (ptpp) REVERT: A 12 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: A 42 GLU cc_start: 0.8504 (tt0) cc_final: 0.7965 (tt0) REVERT: A 234 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8062 (tppt) REVERT: B 4 TRP cc_start: 0.8197 (m100) cc_final: 0.7851 (m-10) REVERT: B 12 ASP cc_start: 0.8927 (m-30) cc_final: 0.8586 (m-30) REVERT: B 42 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 231 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (t) REVERT: C 233 PHE cc_start: 0.8337 (t80) cc_final: 0.7998 (t80) REVERT: E 4 TRP cc_start: 0.8263 (m100) cc_final: 0.7804 (m-10) REVERT: E 12 ASP cc_start: 0.8607 (m-30) cc_final: 0.8327 (m-30) REVERT: F 12 ASP cc_start: 0.8557 (m-30) cc_final: 0.8015 (m-30) REVERT: F 106 LEU cc_start: 0.8645 (tm) cc_final: 0.8400 (tm) REVERT: F 229 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8195 (t80) REVERT: G 4 TRP cc_start: 0.8304 (m100) cc_final: 0.7530 (m-10) REVERT: G 12 ASP cc_start: 0.8577 (m-30) cc_final: 0.8052 (m-30) REVERT: G 234 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8343 (ttmm) REVERT: H 4 TRP cc_start: 0.8256 (m100) cc_final: 0.7591 (m-10) REVERT: H 9 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8869 (ptpp) REVERT: H 42 GLU cc_start: 0.8396 (tt0) cc_final: 0.7975 (tt0) REVERT: I 4 TRP cc_start: 0.8240 (m100) cc_final: 0.7946 (m100) REVERT: I 103 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: I 233 PHE cc_start: 0.7910 (t80) cc_final: 0.7507 (t80) REVERT: J 4 TRP cc_start: 0.8271 (m100) cc_final: 0.7702 (m-10) REVERT: J 42 GLU cc_start: 0.8398 (tt0) cc_final: 0.7947 (tt0) REVERT: J 229 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: J 233 PHE cc_start: 0.8258 (t80) cc_final: 0.7942 (t80) REVERT: K 42 GLU cc_start: 0.8553 (tt0) cc_final: 0.8169 (tt0) REVERT: K 229 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (t80) REVERT: L 4 TRP cc_start: 0.8015 (m100) cc_final: 0.7525 (m-10) REVERT: L 33 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8357 (ttm170) REVERT: L 105 LYS cc_start: 0.8204 (tppt) cc_final: 0.7800 (ttmt) outliers start: 45 outliers final: 30 residues processed: 311 average time/residue: 1.9969 time to fit residues: 721.7780 Evaluate side-chains 321 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J 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 100 MET Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 0.2980 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8763 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23196 Z= 0.150 Angle : 0.530 7.192 30804 Z= 0.255 Chirality : 0.034 0.122 3312 Planarity : 0.003 0.033 3396 Dihedral : 12.534 94.488 6048 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.53 % Allowed : 15.74 % Favored : 82.73 % 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: 3.29 (0.17), residues: 2364 helix: 3.24 (0.11), residues: 1692 sheet: 1.65 (0.45), residues: 132 loop : -1.45 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 25 HIS 0.002 0.001 HIS B 74 PHE 0.019 0.001 PHE E 233 TYR 0.016 0.001 TYR J 17 ARG 0.004 0.000 ARG G 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 2.464 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9272 (mtpt) cc_final: 0.8929 (ptpp) REVERT: A 12 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 42 GLU cc_start: 0.8534 (tt0) cc_final: 0.8120 (tt0) REVERT: B 4 TRP cc_start: 0.8171 (m100) cc_final: 0.7785 (m-10) REVERT: B 12 ASP cc_start: 0.8925 (m-30) cc_final: 0.8586 (m-30) REVERT: B 42 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: C 231 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8019 (t) REVERT: C 233 PHE cc_start: 0.8273 (t80) cc_final: 0.7951 (t80) REVERT: E 4 TRP cc_start: 0.8258 (m100) cc_final: 0.7782 (m-10) REVERT: E 12 ASP cc_start: 0.8579 (m-30) cc_final: 0.8318 (m-30) REVERT: E 231 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8286 (t) REVERT: F 12 ASP cc_start: 0.8560 (m-30) cc_final: 0.8005 (m-30) REVERT: G 4 TRP cc_start: 0.8318 (m100) cc_final: 0.7503 (m-10) REVERT: G 12 ASP cc_start: 0.8565 (m-30) cc_final: 0.8029 (m-30) REVERT: G 231 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8344 (t) REVERT: G 234 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8283 (ttmm) REVERT: H 4 TRP cc_start: 0.8224 (m100) cc_final: 0.7547 (m-10) REVERT: H 9 LYS cc_start: 0.9257 (mtmt) cc_final: 0.8871 (ptpp) REVERT: H 42 GLU cc_start: 0.8393 (tt0) cc_final: 0.7996 (tt0) REVERT: I 4 TRP cc_start: 0.8210 (m100) cc_final: 0.7906 (m100) REVERT: I 104 GLU cc_start: 0.8095 (tp30) cc_final: 0.7520 (tp30) REVERT: J 4 TRP cc_start: 0.8247 (m100) cc_final: 0.7636 (m-10) REVERT: J 42 GLU cc_start: 0.8432 (tt0) cc_final: 0.7955 (tt0) REVERT: J 229 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: J 233 PHE cc_start: 0.8201 (t80) cc_final: 0.7882 (t80) REVERT: K 42 GLU cc_start: 0.8568 (tt0) cc_final: 0.8124 (tt0) REVERT: K 229 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8058 (t80) REVERT: L 4 TRP cc_start: 0.8011 (m100) cc_final: 0.7493 (m-10) REVERT: L 42 GLU cc_start: 0.8436 (tt0) cc_final: 0.8235 (tt0) REVERT: L 105 LYS cc_start: 0.8205 (tppt) cc_final: 0.7799 (ttmt) outliers start: 33 outliers final: 18 residues processed: 316 average time/residue: 1.9767 time to fit residues: 729.9699 Evaluate side-chains 319 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J 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 229 PHE Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.089183 restraints weight = 85549.693| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.70 r_work: 0.2827 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23196 Z= 0.144 Angle : 0.521 6.854 30804 Z= 0.249 Chirality : 0.034 0.135 3312 Planarity : 0.003 0.028 3396 Dihedral : 12.103 92.546 6048 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.30 % Allowed : 16.16 % Favored : 82.55 % 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: 3.47 (0.17), residues: 2364 helix: 3.30 (0.11), residues: 1716 sheet: 1.69 (0.45), residues: 132 loop : -1.35 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 45 HIS 0.001 0.000 HIS I 194 PHE 0.018 0.001 PHE E 233 TYR 0.012 0.001 TYR J 17 ARG 0.003 0.000 ARG G 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12344.37 seconds wall clock time: 211 minutes 32.76 seconds (12692.76 seconds total)