Starting phenix.real_space_refine on Mon Mar 25 09:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_2024/7xqd_33393_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_2024/7xqd_33393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_2024/7xqd_33393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_2024/7xqd_33393_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqd_33393/03_2024/7xqd_33393_trim.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 18.78, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 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: 31.92 Conformation dependent library (CDL) restraints added in 3.8 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: 2.76 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: 13.61 Time building geometry restraints manager: 33.33 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: 99.41 - 106.33: 502 106.33 - 113.25: 49279 113.25 - 120.16: 13950 120.16 - 127.08: 12169 127.08 - 134.00: 228 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 1.850 nonbonded pdb=" OE1 GLU L 111 " pdb=" H GLU L 111 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU J 111 " pdb=" H GLU J 111 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU K 111 " pdb=" H GLU K 111 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU D 111 " pdb=" H GLU D 111 " model vdw 1.619 1.850 ... (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 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: 1.720 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: 0.670 Extract box with map and model: 9.570 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 120.720 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.280 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 12 poor density : 500 time to evaluate : 3.333 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: 2.8290 time to fit residues: 1620.5863 Evaluate side-chains 339 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.197 ------------------------------------------------------------------------------- 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: 0.9980 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8746 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23196 Z= 0.269 Angle : 0.684 7.900 30804 Z= 0.318 Chirality : 0.038 0.148 3312 Planarity : 0.004 0.062 3396 Dihedral : 17.037 110.132 6048 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 10.93 % Favored : 86.06 % 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: 3.32 (0.17), residues: 2364 helix: 3.16 (0.12), residues: 1704 sheet: 2.73 (0.42), residues: 120 loop : -1.40 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 25 HIS 0.003 0.001 HIS F 194 PHE 0.013 0.002 PHE G 52 TYR 0.011 0.002 TYR F 177 ARG 0.009 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 413 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8143 (m100) cc_final: 0.7782 (m-10) REVERT: A 12 ASP cc_start: 0.8586 (m-30) cc_final: 0.8246 (m-30) REVERT: A 42 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 47 ASP cc_start: 0.8980 (p0) cc_final: 0.8759 (p0) REVERT: A 89 THR cc_start: 0.8410 (m) cc_final: 0.8081 (m) REVERT: A 93 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 234 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8091 (tppt) REVERT: B 4 TRP cc_start: 0.8103 (m100) cc_final: 0.7770 (m-10) REVERT: B 12 ASP cc_start: 0.8884 (m-30) cc_final: 0.8535 (m-30) REVERT: B 42 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: C 9 LYS cc_start: 0.9102 (mttt) cc_final: 0.8884 (mttm) REVERT: C 231 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8306 (t) REVERT: C 233 PHE cc_start: 0.8256 (t80) cc_final: 0.7889 (t80) REVERT: E 4 TRP cc_start: 0.8111 (m100) cc_final: 0.7813 (m-10) REVERT: E 12 ASP cc_start: 0.8620 (m-30) cc_final: 0.8379 (m-30) REVERT: E 233 PHE cc_start: 0.7976 (t80) cc_final: 0.7758 (t80) REVERT: F 9 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8462 (ptpp) REVERT: F 12 ASP cc_start: 0.8734 (m-30) cc_final: 0.8170 (m-30) REVERT: G 9 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8859 (mtmm) REVERT: G 12 ASP cc_start: 0.8630 (m-30) cc_final: 0.8119 (m-30) REVERT: H 4 TRP cc_start: 0.8111 (m100) cc_final: 0.7530 (m-10) REVERT: H 42 GLU cc_start: 0.8318 (tt0) cc_final: 0.7794 (tt0) REVERT: I 4 TRP cc_start: 0.8134 (m100) cc_final: 0.7859 (m100) REVERT: I 233 PHE cc_start: 0.7803 (t80) cc_final: 0.7542 (t80) REVERT: J 4 TRP cc_start: 0.8000 (m100) cc_final: 0.7594 (m-10) REVERT: J 7 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8589 (tt) REVERT: J 42 GLU cc_start: 0.8297 (tt0) cc_final: 0.7667 (tt0) REVERT: J 104 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7386 (mp0) REVERT: J 229 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: J 230 TYR cc_start: 0.8639 (t80) cc_final: 0.8343 (t80) REVERT: J 233 PHE cc_start: 0.8280 (t80) cc_final: 0.7924 (t80) REVERT: K 12 ASP cc_start: 0.8527 (m-30) cc_final: 0.8268 (m-30) REVERT: K 42 GLU cc_start: 0.8469 (tt0) cc_final: 0.7967 (tt0) REVERT: L 4 TRP cc_start: 0.7986 (m100) cc_final: 0.7535 (m-10) REVERT: L 33 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8118 (ttm170) outliers start: 65 outliers final: 25 residues processed: 382 average time/residue: 2.4431 time to fit residues: 1089.1495 Evaluate side-chains 359 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 327 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 93 LEU 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 220 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER 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 220 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: 7.9990 chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8744 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23196 Z= 0.188 Angle : 0.550 7.002 30804 Z= 0.263 Chirality : 0.035 0.118 3312 Planarity : 0.003 0.033 3396 Dihedral : 15.227 93.582 6048 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.78 % Allowed : 12.04 % Favored : 85.19 % 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: 3.44 (0.17), residues: 2364 helix: 3.29 (0.11), residues: 1704 sheet: 1.81 (0.45), residues: 132 loop : -1.30 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 25 HIS 0.002 0.001 HIS L 194 PHE 0.010 0.001 PHE B 30 TYR 0.009 0.001 TYR A 66 ARG 0.001 0.000 ARG K 153 *********************** 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 394 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 334 time to evaluate : 3.379 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8204 (m100) cc_final: 0.7805 (m-10) REVERT: A 12 ASP cc_start: 0.8720 (m-30) cc_final: 0.7927 (m-30) REVERT: A 42 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: A 89 THR cc_start: 0.8463 (m) cc_final: 0.8154 (m) REVERT: A 234 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8075 (tppt) REVERT: B 4 TRP cc_start: 0.8161 (m100) cc_final: 0.7833 (m-10) REVERT: B 12 ASP cc_start: 0.8894 (m-30) cc_final: 0.8546 (m-30) REVERT: B 42 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: C 9 LYS cc_start: 0.9103 (mttt) cc_final: 0.8838 (mttm) REVERT: C 231 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8264 (t) REVERT: C 233 PHE cc_start: 0.8212 (t80) cc_final: 0.7851 (t80) REVERT: D 4 TRP cc_start: 0.8403 (m100) cc_final: 0.7966 (m-10) REVERT: E 4 TRP cc_start: 0.8153 (m100) cc_final: 0.7858 (m-10) REVERT: E 12 ASP cc_start: 0.8598 (m-30) cc_final: 0.8392 (m-30) REVERT: E 233 PHE cc_start: 0.7987 (t80) cc_final: 0.7764 (t80) REVERT: F 12 ASP cc_start: 0.8667 (m-30) cc_final: 0.8065 (m-30) REVERT: G 4 TRP cc_start: 0.8257 (m100) cc_final: 0.7500 (m-90) REVERT: G 12 ASP cc_start: 0.8617 (m-30) cc_final: 0.8085 (m-30) REVERT: H 4 TRP cc_start: 0.8154 (m100) cc_final: 0.7545 (m-10) REVERT: H 42 GLU cc_start: 0.8290 (tt0) cc_final: 0.7887 (tt0) REVERT: H 153 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7747 (ptp90) REVERT: I 4 TRP cc_start: 0.8136 (m100) cc_final: 0.7876 (m100) REVERT: I 233 PHE cc_start: 0.7835 (t80) cc_final: 0.7536 (t80) REVERT: J 4 TRP cc_start: 0.8050 (m100) cc_final: 0.7643 (m-10) REVERT: J 42 GLU cc_start: 0.8338 (tt0) cc_final: 0.7712 (tt0) REVERT: J 229 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: J 230 TYR cc_start: 0.8595 (t80) cc_final: 0.8329 (t80) REVERT: J 233 PHE cc_start: 0.8257 (t80) cc_final: 0.7909 (t80) REVERT: K 12 ASP cc_start: 0.8523 (m-30) cc_final: 0.8269 (m-30) REVERT: K 42 GLU cc_start: 0.8439 (tt0) cc_final: 0.7916 (tt0) REVERT: L 4 TRP cc_start: 0.8016 (m100) cc_final: 0.7560 (m-10) REVERT: L 33 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8201 (ttm170) outliers start: 60 outliers final: 30 residues processed: 357 average time/residue: 2.4531 time to fit residues: 1015.1665 Evaluate side-chains 353 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 317 time to evaluate : 2.969 ------------------------------------------------------------------------------- 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 39 THR 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 39 THR Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 39 THR 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 93 LEU Chi-restraints excluded: chain K residue 105 LYS 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 93 LEU Chi-restraints excluded: chain L residue 160 LEU 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: 0.0970 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.8765 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23196 Z= 0.223 Angle : 0.557 7.772 30804 Z= 0.272 Chirality : 0.035 0.125 3312 Planarity : 0.003 0.034 3396 Dihedral : 14.480 89.794 6048 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.45 % Allowed : 12.64 % Favored : 84.91 % 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: 3.39 (0.17), residues: 2364 helix: 3.25 (0.11), residues: 1704 sheet: 1.79 (0.45), residues: 132 loop : -1.33 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 25 HIS 0.002 0.001 HIS L 194 PHE 0.011 0.001 PHE I 32 TYR 0.014 0.001 TYR J 17 ARG 0.001 0.000 ARG F 33 *********************** 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 380 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 327 time to evaluate : 3.770 Fit side-chains revert: symmetry clash REVERT: A 4 TRP cc_start: 0.8202 (m100) cc_final: 0.7804 (m-10) REVERT: A 9 LYS cc_start: 0.9236 (mtpt) cc_final: 0.8890 (ptpp) REVERT: A 12 ASP cc_start: 0.8647 (m-30) cc_final: 0.8266 (m-30) REVERT: A 42 GLU cc_start: 0.8513 (tt0) cc_final: 0.8032 (tt0) REVERT: A 234 LYS cc_start: 0.8328 (ttpp) cc_final: 0.8061 (tppt) REVERT: B 4 TRP cc_start: 0.8216 (m100) cc_final: 0.7835 (m-10) REVERT: B 12 ASP cc_start: 0.8883 (m-30) cc_final: 0.8516 (m-30) REVERT: B 42 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: C 9 LYS cc_start: 0.9135 (mttt) cc_final: 0.8885 (mttm) REVERT: C 231 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (t) REVERT: C 233 PHE cc_start: 0.8249 (t80) cc_final: 0.7891 (t80) REVERT: D 4 TRP cc_start: 0.8412 (m100) cc_final: 0.7959 (m-10) REVERT: E 4 TRP cc_start: 0.8146 (m100) cc_final: 0.7827 (m-10) REVERT: E 12 ASP cc_start: 0.8633 (m-30) cc_final: 0.8387 (m-30) REVERT: E 233 PHE cc_start: 0.7975 (t80) cc_final: 0.7734 (t80) REVERT: F 12 ASP cc_start: 0.8672 (m-30) cc_final: 0.8102 (m-30) REVERT: G 4 TRP cc_start: 0.8208 (m100) cc_final: 0.7463 (m-90) REVERT: G 9 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8908 (mttt) REVERT: G 12 ASP cc_start: 0.8588 (m-30) cc_final: 0.8057 (m-30) REVERT: G 234 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8437 (ttmm) REVERT: H 4 TRP cc_start: 0.8177 (m100) cc_final: 0.7571 (m-10) REVERT: H 42 GLU cc_start: 0.8262 (tt0) cc_final: 0.7905 (tt0) REVERT: I 4 TRP cc_start: 0.8177 (m100) cc_final: 0.7938 (m100) REVERT: I 103 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: I 233 PHE cc_start: 0.7858 (t80) cc_final: 0.7542 (t80) REVERT: J 4 TRP cc_start: 0.8112 (m100) cc_final: 0.7676 (m-10) REVERT: J 42 GLU cc_start: 0.8375 (tt0) cc_final: 0.7800 (tt0) REVERT: J 229 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: J 233 PHE cc_start: 0.8264 (t80) cc_final: 0.7919 (t80) REVERT: K 12 ASP cc_start: 0.8535 (m-30) cc_final: 0.8293 (m-30) REVERT: K 42 GLU cc_start: 0.8531 (tt0) cc_final: 0.8039 (tt0) REVERT: K 104 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8267 (tm-30) REVERT: L 4 TRP cc_start: 0.8018 (m100) cc_final: 0.7563 (m-10) REVERT: L 33 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8216 (ttm170) outliers start: 53 outliers final: 27 residues processed: 352 average time/residue: 2.5085 time to fit residues: 1030.7004 Evaluate side-chains 350 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 3.590 ------------------------------------------------------------------------------- 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 39 THR 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 H residue 231 VAL Chi-restraints excluded: chain I residue 39 THR 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 34 ILE 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 93 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.8798 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23196 Z= 0.295 Angle : 0.607 7.959 30804 Z= 0.300 Chirality : 0.037 0.137 3312 Planarity : 0.004 0.041 3396 Dihedral : 14.466 92.759 6048 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.87 % Allowed : 12.82 % 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: 3.10 (0.16), residues: 2364 helix: 3.02 (0.11), residues: 1704 sheet: 1.70 (0.45), residues: 132 loop : -1.39 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 25 HIS 0.003 0.001 HIS L 194 PHE 0.013 0.002 PHE B 52 TYR 0.014 0.002 TYR J 17 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 376 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 3.126 Fit side-chains REVERT: A 4 TRP cc_start: 0.8208 (m100) cc_final: 0.7778 (m-10) REVERT: A 9 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8893 (ptpp) REVERT: A 12 ASP cc_start: 0.8712 (m-30) cc_final: 0.8189 (m-30) REVERT: A 42 GLU cc_start: 0.8529 (tt0) cc_final: 0.7988 (tt0) REVERT: A 234 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8060 (tppt) REVERT: B 4 TRP cc_start: 0.8215 (m100) cc_final: 0.7857 (m-10) REVERT: B 12 ASP cc_start: 0.8888 (m-30) cc_final: 0.8512 (m-30) REVERT: B 42 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: C 9 LYS cc_start: 0.9159 (mttt) cc_final: 0.8887 (mttm) REVERT: C 231 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8314 (t) REVERT: C 233 PHE cc_start: 0.8330 (t80) cc_final: 0.7990 (t80) REVERT: D 4 TRP cc_start: 0.8411 (m100) cc_final: 0.7949 (m-10) REVERT: E 4 TRP cc_start: 0.8208 (m100) cc_final: 0.7847 (m-10) REVERT: E 12 ASP cc_start: 0.8623 (m-30) cc_final: 0.8332 (m-30) REVERT: F 12 ASP cc_start: 0.8581 (m-30) cc_final: 0.8032 (m-30) REVERT: G 4 TRP cc_start: 0.8194 (m100) cc_final: 0.7407 (m-90) REVERT: G 12 ASP cc_start: 0.8553 (m-30) cc_final: 0.8031 (m-30) REVERT: G 231 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (t) REVERT: H 4 TRP cc_start: 0.8264 (m100) cc_final: 0.7662 (m-10) REVERT: H 42 GLU cc_start: 0.8350 (tt0) cc_final: 0.7915 (tt0) REVERT: I 4 TRP cc_start: 0.8157 (m100) cc_final: 0.7907 (m100) REVERT: I 103 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: I 233 PHE cc_start: 0.7912 (t80) cc_final: 0.7575 (t80) REVERT: J 4 TRP cc_start: 0.8170 (m100) cc_final: 0.7675 (m-10) REVERT: J 42 GLU cc_start: 0.8403 (tt0) cc_final: 0.7895 (tt0) REVERT: J 229 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: J 233 PHE cc_start: 0.8281 (t80) cc_final: 0.7960 (t80) REVERT: K 12 ASP cc_start: 0.8550 (m-30) cc_final: 0.8321 (m-30) REVERT: K 42 GLU cc_start: 0.8481 (tt0) cc_final: 0.8035 (tt0) REVERT: K 104 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8228 (tm-30) REVERT: L 4 TRP cc_start: 0.8015 (m100) cc_final: 0.7564 (m-10) REVERT: L 33 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8319 (ttm170) REVERT: L 105 LYS cc_start: 0.8237 (tppt) cc_final: 0.7858 (tttt) outliers start: 62 outliers final: 26 residues processed: 343 average time/residue: 2.4565 time to fit residues: 977.2128 Evaluate side-chains 330 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 298 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 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 39 THR Chi-restraints excluded: chain G residue 231 VAL 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 H residue 231 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.0060 chunk 121 optimal weight: 5.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- 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: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23196 Z= 0.180 Angle : 0.548 7.800 30804 Z= 0.265 Chirality : 0.034 0.113 3312 Planarity : 0.003 0.035 3396 Dihedral : 13.826 92.462 6048 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 13.75 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.17), residues: 2364 helix: 3.17 (0.11), residues: 1704 sheet: 1.68 (0.45), residues: 132 loop : -1.39 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 25 HIS 0.002 0.001 HIS L 194 PHE 0.016 0.001 PHE E 233 TYR 0.015 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 350 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 301 time to evaluate : 3.418 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8898 (ptpp) REVERT: A 12 ASP cc_start: 0.8664 (m-30) cc_final: 0.8190 (m-30) REVERT: A 42 GLU cc_start: 0.8519 (tt0) cc_final: 0.7929 (tt0) REVERT: A 234 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8062 (tppt) REVERT: B 4 TRP cc_start: 0.8223 (m100) cc_final: 0.7854 (m-10) REVERT: B 12 ASP cc_start: 0.8886 (m-30) cc_final: 0.8521 (m-30) REVERT: B 42 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: C 9 LYS cc_start: 0.9159 (mttt) cc_final: 0.8879 (mttm) REVERT: C 231 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (t) REVERT: C 233 PHE cc_start: 0.8300 (t80) cc_final: 0.7967 (t80) REVERT: D 4 TRP cc_start: 0.8366 (m100) cc_final: 0.7890 (m-10) REVERT: E 4 TRP cc_start: 0.8215 (m100) cc_final: 0.7829 (m-10) REVERT: E 12 ASP cc_start: 0.8610 (m-30) cc_final: 0.8319 (m-30) REVERT: F 12 ASP cc_start: 0.8580 (m-30) cc_final: 0.7992 (m-30) REVERT: G 4 TRP cc_start: 0.8199 (m100) cc_final: 0.7417 (m-10) REVERT: G 12 ASP cc_start: 0.8553 (m-30) cc_final: 0.8013 (m-30) REVERT: H 4 TRP cc_start: 0.8311 (m100) cc_final: 0.7671 (m-10) REVERT: H 42 GLU cc_start: 0.8327 (tt0) cc_final: 0.7915 (tt0) REVERT: I 4 TRP cc_start: 0.8163 (m100) cc_final: 0.7860 (m100) REVERT: I 103 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: I 233 PHE cc_start: 0.7901 (t80) cc_final: 0.7552 (t80) REVERT: J 4 TRP cc_start: 0.8237 (m100) cc_final: 0.7745 (m-10) REVERT: J 42 GLU cc_start: 0.8417 (tt0) cc_final: 0.7903 (tt0) REVERT: J 229 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: J 233 PHE cc_start: 0.8280 (t80) cc_final: 0.7954 (t80) REVERT: K 12 ASP cc_start: 0.8528 (m-30) cc_final: 0.8327 (m-30) REVERT: K 42 GLU cc_start: 0.8510 (tt0) cc_final: 0.8071 (tt0) REVERT: K 104 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8216 (tm-30) REVERT: L 4 TRP cc_start: 0.8016 (m100) cc_final: 0.7543 (m-10) REVERT: L 33 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8328 (ttm170) REVERT: L 105 LYS cc_start: 0.8251 (tppt) cc_final: 0.7859 (tttt) outliers start: 49 outliers final: 24 residues processed: 326 average time/residue: 2.4277 time to fit residues: 929.9160 Evaluate side-chains 325 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 34 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 39 THR 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 157 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 K residue 100 MET Chi-restraints excluded: chain K residue 105 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.8803 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23196 Z= 0.319 Angle : 0.606 7.846 30804 Z= 0.297 Chirality : 0.037 0.136 3312 Planarity : 0.004 0.040 3396 Dihedral : 14.081 95.577 6048 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.41 % Allowed : 14.07 % Favored : 83.52 % 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: 3.02 (0.16), residues: 2364 helix: 2.98 (0.11), residues: 1704 sheet: 1.63 (0.45), residues: 132 loop : -1.44 (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 0.019 0.002 PHE E 233 TYR 0.015 0.002 TYR J 17 ARG 0.003 0.000 ARG G 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 349 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 297 time to evaluate : 3.889 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8885 (ptpp) REVERT: A 12 ASP cc_start: 0.8681 (m-30) cc_final: 0.8177 (m-30) REVERT: A 42 GLU cc_start: 0.8525 (tt0) cc_final: 0.7932 (tt0) REVERT: A 234 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8074 (tppt) REVERT: B 4 TRP cc_start: 0.8242 (m100) cc_final: 0.7886 (m-10) REVERT: B 12 ASP cc_start: 0.8927 (m-30) cc_final: 0.8573 (m-30) REVERT: B 42 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 9 LYS cc_start: 0.9171 (mttt) cc_final: 0.8871 (mttm) REVERT: C 231 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (t) REVERT: C 233 PHE cc_start: 0.8354 (t80) cc_final: 0.8000 (t80) REVERT: D 4 TRP cc_start: 0.8402 (m100) cc_final: 0.7959 (m-10) REVERT: E 4 TRP cc_start: 0.8243 (m100) cc_final: 0.7834 (m-10) REVERT: E 12 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: F 12 ASP cc_start: 0.8539 (m-30) cc_final: 0.8011 (m-30) REVERT: G 4 TRP cc_start: 0.8194 (m100) cc_final: 0.7430 (m-10) REVERT: G 12 ASP cc_start: 0.8525 (m-30) cc_final: 0.8007 (m-30) REVERT: G 234 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8380 (ttmm) REVERT: H 4 TRP cc_start: 0.8316 (m100) cc_final: 0.7629 (m-10) REVERT: H 9 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8882 (ptpp) REVERT: H 42 GLU cc_start: 0.8348 (tt0) cc_final: 0.7934 (tt0) REVERT: I 4 TRP cc_start: 0.8137 (m100) cc_final: 0.7849 (m100) REVERT: I 103 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: I 233 PHE cc_start: 0.7950 (t80) cc_final: 0.7577 (t80) REVERT: J 4 TRP cc_start: 0.8267 (m100) cc_final: 0.7762 (m-10) REVERT: J 9 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9123 (mttp) REVERT: J 42 GLU cc_start: 0.8392 (tt0) cc_final: 0.7933 (tt0) REVERT: J 229 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: J 233 PHE cc_start: 0.8279 (t80) cc_final: 0.7961 (t80) REVERT: K 12 ASP cc_start: 0.8548 (m-30) cc_final: 0.8336 (m-30) REVERT: K 42 GLU cc_start: 0.8571 (tt0) cc_final: 0.8130 (tt0) REVERT: K 104 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8211 (tm-30) REVERT: K 229 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (t80) REVERT: L 4 TRP cc_start: 0.8029 (m100) cc_final: 0.7561 (m-10) REVERT: L 105 LYS cc_start: 0.8244 (tppt) cc_final: 0.7846 (ttmt) outliers start: 52 outliers final: 30 residues processed: 320 average time/residue: 2.4902 time to fit residues: 921.3031 Evaluate side-chains 329 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 3.735 ------------------------------------------------------------------------------- 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 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 12 ASP 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 39 THR Chi-restraints excluded: chain G residue 190 ASP 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 106 LEU Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER 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=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: 3.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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: 0.8794 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23196 Z= 0.247 Angle : 0.574 7.604 30804 Z= 0.281 Chirality : 0.035 0.122 3312 Planarity : 0.004 0.037 3396 Dihedral : 13.849 95.920 6048 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 14.17 % Favored : 83.38 % 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: 3.03 (0.16), residues: 2364 helix: 3.14 (0.11), residues: 1668 sheet: 1.63 (0.45), residues: 132 loop : -1.68 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 25 HIS 0.002 0.001 HIS L 194 PHE 0.019 0.002 PHE E 233 TYR 0.014 0.001 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 345 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 292 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8927 (ptpp) REVERT: A 12 ASP cc_start: 0.8653 (m-30) cc_final: 0.8147 (m-30) REVERT: A 42 GLU cc_start: 0.8540 (tt0) cc_final: 0.8016 (tt0) REVERT: A 234 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8064 (tppt) REVERT: B 4 TRP cc_start: 0.8200 (m100) cc_final: 0.7861 (m-10) REVERT: B 12 ASP cc_start: 0.8918 (m-30) cc_final: 0.8556 (m-30) REVERT: B 42 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: C 9 LYS cc_start: 0.9171 (mttt) cc_final: 0.8871 (mttm) REVERT: C 231 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8179 (t) REVERT: C 233 PHE cc_start: 0.8354 (t80) cc_final: 0.8026 (t80) REVERT: D 4 TRP cc_start: 0.8377 (m100) cc_final: 0.7921 (m-10) REVERT: E 4 TRP cc_start: 0.8253 (m100) cc_final: 0.7834 (m-10) REVERT: E 12 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: F 12 ASP cc_start: 0.8518 (m-30) cc_final: 0.7981 (m-30) REVERT: G 4 TRP cc_start: 0.8230 (m100) cc_final: 0.7462 (m-10) REVERT: G 12 ASP cc_start: 0.8510 (m-30) cc_final: 0.7986 (m-30) REVERT: G 231 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8446 (t) REVERT: G 234 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8345 (ttmm) REVERT: H 4 TRP cc_start: 0.8316 (m100) cc_final: 0.7611 (m-10) REVERT: H 9 LYS cc_start: 0.9268 (mtmt) cc_final: 0.8857 (ptpp) REVERT: H 42 GLU cc_start: 0.8368 (tt0) cc_final: 0.7968 (tt0) REVERT: I 4 TRP cc_start: 0.8157 (m100) cc_final: 0.7864 (m100) REVERT: I 103 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: I 233 PHE cc_start: 0.7951 (t80) cc_final: 0.7551 (t80) REVERT: J 4 TRP cc_start: 0.8249 (m100) cc_final: 0.7718 (m-10) REVERT: J 9 LYS cc_start: 0.9334 (mtpt) cc_final: 0.9109 (mttp) REVERT: J 42 GLU cc_start: 0.8387 (tt0) cc_final: 0.7924 (tt0) REVERT: J 229 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: J 233 PHE cc_start: 0.8265 (t80) cc_final: 0.7955 (t80) REVERT: K 42 GLU cc_start: 0.8579 (tt0) cc_final: 0.8143 (tt0) REVERT: K 229 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8113 (t80) REVERT: L 4 TRP cc_start: 0.8033 (m100) cc_final: 0.7573 (m-10) REVERT: L 105 LYS cc_start: 0.8240 (tppt) cc_final: 0.7826 (ttmt) outliers start: 53 outliers final: 31 residues processed: 317 average time/residue: 2.4880 time to fit residues: 925.8822 Evaluate side-chains 332 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 3.487 ------------------------------------------------------------------------------- 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 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 12 ASP 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 39 THR Chi-restraints excluded: chain G residue 190 ASP 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 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 106 LEU Chi-restraints excluded: chain J residue 157 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 K residue 100 MET Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23196 Z= 0.319 Angle : 0.606 7.450 30804 Z= 0.298 Chirality : 0.037 0.191 3312 Planarity : 0.004 0.041 3396 Dihedral : 13.987 98.476 6048 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 14.72 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.16), residues: 2364 helix: 2.96 (0.11), residues: 1680 sheet: 1.59 (0.44), residues: 132 loop : -1.62 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 25 HIS 0.002 0.001 HIS I 194 PHE 0.020 0.002 PHE E 233 TYR 0.015 0.002 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 343 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 3.324 Fit side-chains REVERT: A 9 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8937 (ptpp) REVERT: A 12 ASP cc_start: 0.8650 (m-30) cc_final: 0.8181 (m-30) REVERT: A 42 GLU cc_start: 0.8530 (tt0) cc_final: 0.8004 (tt0) REVERT: A 234 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8063 (tppt) REVERT: B 4 TRP cc_start: 0.8204 (m100) cc_final: 0.7847 (m-10) REVERT: B 12 ASP cc_start: 0.8915 (m-30) cc_final: 0.8572 (m-30) REVERT: B 42 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: C 9 LYS cc_start: 0.9176 (mttt) cc_final: 0.8887 (mttm) REVERT: C 231 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (t) REVERT: C 233 PHE cc_start: 0.8374 (t80) cc_final: 0.8062 (t80) REVERT: D 4 TRP cc_start: 0.8411 (m100) cc_final: 0.7969 (m-10) REVERT: E 4 TRP cc_start: 0.8262 (m100) cc_final: 0.7825 (m-10) REVERT: E 12 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: F 12 ASP cc_start: 0.8521 (m-30) cc_final: 0.7980 (m-30) REVERT: F 229 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8199 (t80) REVERT: G 4 TRP cc_start: 0.8208 (m100) cc_final: 0.7430 (m-10) REVERT: G 12 ASP cc_start: 0.8519 (m-30) cc_final: 0.8008 (m-30) REVERT: G 231 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8466 (t) REVERT: H 4 TRP cc_start: 0.8281 (m100) cc_final: 0.7620 (m-10) REVERT: H 42 GLU cc_start: 0.8393 (tt0) cc_final: 0.7989 (tt0) REVERT: I 4 TRP cc_start: 0.8212 (m100) cc_final: 0.7897 (m100) REVERT: I 103 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: I 233 PHE cc_start: 0.7937 (t80) cc_final: 0.7534 (t80) REVERT: J 4 TRP cc_start: 0.8265 (m100) cc_final: 0.7648 (m-10) REVERT: J 42 GLU cc_start: 0.8377 (tt0) cc_final: 0.7954 (tt0) REVERT: J 229 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: J 233 PHE cc_start: 0.8276 (t80) cc_final: 0.7970 (t80) REVERT: K 42 GLU cc_start: 0.8581 (tt0) cc_final: 0.8148 (tt0) REVERT: K 229 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8104 (t80) REVERT: L 4 TRP cc_start: 0.8032 (m100) cc_final: 0.7525 (m-10) REVERT: L 105 LYS cc_start: 0.8204 (tppt) cc_final: 0.7798 (ttmt) outliers start: 45 outliers final: 31 residues processed: 322 average time/residue: 2.4659 time to fit residues: 921.5778 Evaluate side-chains 326 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 287 time to evaluate : 3.462 ------------------------------------------------------------------------------- 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 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 E residue 12 ASP 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 229 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 34 ILE 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 106 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 106 LEU 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 229 PHE Chi-restraints excluded: chain L residue 18 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8770 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23196 Z= 0.157 Angle : 0.537 7.255 30804 Z= 0.259 Chirality : 0.034 0.130 3312 Planarity : 0.003 0.034 3396 Dihedral : 13.180 96.532 6048 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.67 % Allowed : 15.42 % Favored : 82.92 % 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: 3.20 (0.17), residues: 2364 helix: 3.18 (0.11), residues: 1692 sheet: 1.68 (0.45), residues: 132 loop : -1.54 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 4 HIS 0.002 0.001 HIS L 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 340 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 3.459 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9241 (mtpt) cc_final: 0.8927 (ptpp) REVERT: A 12 ASP cc_start: 0.8626 (m-30) cc_final: 0.8111 (m-30) REVERT: A 42 GLU cc_start: 0.8546 (tt0) cc_final: 0.8086 (tt0) REVERT: B 4 TRP cc_start: 0.8209 (m100) cc_final: 0.7836 (m-10) REVERT: B 12 ASP cc_start: 0.8902 (m-30) cc_final: 0.8552 (m-30) REVERT: B 42 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: C 9 LYS cc_start: 0.9159 (mttt) cc_final: 0.8894 (mttm) REVERT: C 231 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8079 (t) REVERT: C 233 PHE cc_start: 0.8324 (t80) cc_final: 0.7997 (t80) REVERT: D 4 TRP cc_start: 0.8383 (m100) cc_final: 0.7927 (m-10) REVERT: E 4 TRP cc_start: 0.8230 (m100) cc_final: 0.7791 (m-10) REVERT: E 12 ASP cc_start: 0.8543 (m-30) cc_final: 0.8289 (m-30) REVERT: F 12 ASP cc_start: 0.8494 (m-30) cc_final: 0.7917 (m-30) REVERT: G 4 TRP cc_start: 0.8201 (m100) cc_final: 0.7397 (m-10) REVERT: G 12 ASP cc_start: 0.8504 (m-30) cc_final: 0.7968 (m-30) REVERT: G 231 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8419 (t) REVERT: H 4 TRP cc_start: 0.8257 (m100) cc_final: 0.7642 (m-10) REVERT: H 9 LYS cc_start: 0.9268 (mtmt) cc_final: 0.8877 (ptpp) REVERT: H 42 GLU cc_start: 0.8369 (tt0) cc_final: 0.7959 (tt0) REVERT: I 4 TRP cc_start: 0.8219 (m100) cc_final: 0.7897 (m100) REVERT: I 233 PHE cc_start: 0.7874 (t80) cc_final: 0.7460 (t80) REVERT: J 4 TRP cc_start: 0.8229 (m100) cc_final: 0.7632 (m-10) REVERT: J 42 GLU cc_start: 0.8377 (tt0) cc_final: 0.7923 (tt0) REVERT: J 229 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: J 233 PHE cc_start: 0.8255 (t80) cc_final: 0.7948 (t80) REVERT: K 42 GLU cc_start: 0.8596 (tt0) cc_final: 0.8166 (tt0) REVERT: K 229 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8111 (t80) REVERT: L 4 TRP cc_start: 0.8021 (m100) cc_final: 0.7506 (m-10) REVERT: L 105 LYS cc_start: 0.8206 (tppt) cc_final: 0.7799 (ttmt) outliers start: 36 outliers final: 25 residues processed: 322 average time/residue: 2.5212 time to fit residues: 958.6662 Evaluate side-chains 321 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 291 time to evaluate : 3.538 ------------------------------------------------------------------------------- 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 31 ILE 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 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 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 39 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 93 LEU 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 106 LEU 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 160 LEU 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: 4.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.127337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.088861 restraints weight = 85424.501| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.71 r_work: 0.2816 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4222 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= 0.148 Angle : 0.527 7.424 30804 Z= 0.253 Chirality : 0.034 0.136 3312 Planarity : 0.003 0.030 3396 Dihedral : 12.739 96.053 6048 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.30 % Allowed : 16.25 % Favored : 82.45 % 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: 3.39 (0.17), residues: 2364 helix: 3.26 (0.11), residues: 1716 sheet: 1.70 (0.45), residues: 132 loop : -1.42 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 25 HIS 0.001 0.000 HIS I 194 PHE 0.019 0.001 PHE E 233 TYR 0.015 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: 15453.57 seconds wall clock time: 269 minutes 44.73 seconds (16184.73 seconds total)