Starting phenix.real_space_refine on Sun Feb 25 02:08:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqf_33394/02_2024/7xqf_33394_trim.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 12 5.49 5 S 96 5.16 5 C 15912 2.51 5 N 3132 2.21 5 O 4020 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-5238/modules/chem_data/mon_lib" Total number of atoms: 43140 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: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "F" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "G" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "H" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "I" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "J" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "K" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "L" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 254 Unusual residues: {'C14': 11, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "L" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Time building chain proxies: 18.75, per 1000 atoms: 0.43 Number of scatterers: 43140 At special positions: 0 Unit cell: (107.696, 111.088, 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 12 15.00 O 4020 8.00 N 3132 7.00 C 15912 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: 30.73 Conformation dependent library (CDL) restraints added in 3.7 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: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.868A pdb=" N LYS A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.868A pdb=" N LYS B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.868A pdb=" N LYS C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.172A 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: 3.868A pdb=" N LYS D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.172A 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: 3.869A pdb=" N LYS E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.554A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.868A pdb=" N LYS F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.172A 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: 3.868A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.554A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.868A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.775A 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: 4.171A 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: 3.868A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.554A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.869A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.773A 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: 4.172A 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: 3.868A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.171A 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: 3.869A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.555A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.172A 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: 3.505A 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: 3.505A 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: 3.506A 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: 3.505A 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: 3.506A 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: 3.505A 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: 3.505A 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: 3.505A 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: 3.506A 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: 3.505A 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: 3.506A 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: 3.506A 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: 14.76 Time building geometry restraints manager: 31.70 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: 48 1.23 - 1.42: 8808 1.42 - 1.62: 14124 1.62 - 1.81: 144 Bond restraints: 43092 Sorted by residual: bond pdb=" C8 PTY B 311 " pdb=" O7 PTY B 311 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C8 PTY C 311 " pdb=" O7 PTY C 311 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C8 PTY J 311 " pdb=" O7 PTY J 311 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C8 PTY F 311 " pdb=" O7 PTY F 311 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C8 PTY D 311 " pdb=" O7 PTY D 311 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 43087 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 630 106.93 - 113.70: 49741 113.70 - 120.47: 14855 120.47 - 127.24: 10529 127.24 - 134.01: 217 Bond angle restraints: 75972 Sorted by residual: angle pdb=" O11 PTY L 311 " pdb=" P1 PTY L 311 " pdb=" O14 PTY L 311 " ideal model delta sigma weight residual 92.90 109.31 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" O11 PTY B 311 " pdb=" P1 PTY B 311 " pdb=" O14 PTY B 311 " ideal model delta sigma weight residual 92.90 109.30 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" O11 PTY G 311 " pdb=" P1 PTY G 311 " pdb=" O14 PTY G 311 " ideal model delta sigma weight residual 92.90 109.29 -16.39 3.00e+00 1.11e-01 2.99e+01 angle pdb=" O11 PTY I 311 " pdb=" P1 PTY I 311 " pdb=" O14 PTY I 311 " ideal model delta sigma weight residual 92.90 109.28 -16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O11 PTY E 311 " pdb=" P1 PTY E 311 " pdb=" O14 PTY E 311 " ideal model delta sigma weight residual 92.90 109.28 -16.38 3.00e+00 1.11e-01 2.98e+01 ... (remaining 75967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 20755 22.50 - 45.01: 1049 45.01 - 67.51: 360 67.51 - 90.01: 60 90.01 - 112.52: 48 Dihedral angle restraints: 22272 sinusoidal: 13296 harmonic: 8976 Sorted by residual: dihedral pdb=" CAR Y01 G 313 " pdb=" CAV Y01 G 313 " pdb=" CBC Y01 G 313 " pdb=" CAZ Y01 G 313 " ideal model delta sinusoidal sigma weight residual 55.40 -57.12 112.52 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CAR Y01 D 313 " pdb=" CAV Y01 D 313 " pdb=" CBC Y01 D 313 " pdb=" CAZ Y01 D 313 " ideal model delta sinusoidal sigma weight residual 55.40 -57.09 112.49 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" CAR Y01 K 313 " pdb=" CAV Y01 K 313 " pdb=" CBC Y01 K 313 " pdb=" CAZ Y01 K 313 " ideal model delta sinusoidal sigma weight residual 55.40 -57.07 112.47 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2486 0.040 - 0.079: 644 0.079 - 0.119: 146 0.119 - 0.159: 12 0.159 - 0.199: 12 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CBC Y01 G 312 " pdb=" CAR Y01 G 312 " pdb=" CAV Y01 G 312 " pdb=" OAW Y01 G 312 " both_signs ideal model delta sigma weight residual False -2.54 -2.35 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CBC Y01 B 312 " pdb=" CAR Y01 B 312 " pdb=" CAV Y01 B 312 " pdb=" OAW Y01 B 312 " both_signs ideal model delta sigma weight residual False -2.54 -2.35 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CBC Y01 L 312 " pdb=" CAR Y01 L 312 " pdb=" CAV Y01 L 312 " pdb=" OAW Y01 L 312 " both_signs ideal model delta sigma weight residual False -2.54 -2.35 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 3297 not shown) Planarity restraints: 5688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 101 " 0.028 9.50e-02 1.11e+02 1.22e-02 1.51e+00 pdb=" NE ARG D 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 101 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 101 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 101 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG D 101 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG D 101 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 101 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 101 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 87 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO E 88 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 88 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 88 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 87 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO G 88 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " 0.015 5.00e-02 4.00e+02 ... (remaining 5685 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 339 2.08 - 2.71: 64374 2.71 - 3.34: 115652 3.34 - 3.97: 142614 3.97 - 4.60: 235545 Nonbonded interactions: 558524 Sorted by model distance: nonbonded pdb=" OD2 ASP B 3 " pdb=" HE1 TRP C 4 " model vdw 1.455 1.850 nonbonded pdb=" OD2 ASP H 3 " pdb=" HE1 TRP I 4 " model vdw 1.477 1.850 nonbonded pdb="HD22 ASN G 63 " pdb=" O HOH H 362 " model vdw 1.486 1.850 nonbonded pdb=" OD2 ASP G 3 " pdb=" HE1 TRP H 4 " model vdw 1.493 1.850 nonbonded pdb=" OD2 ASP C 3 " pdb=" HE1 TRP D 4 " model vdw 1.510 1.850 ... (remaining 558519 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.740 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: 0.710 Extract box with map and model: 9.600 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 119.080 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.300 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.005 0.071 23124 Z= 0.316 Angle : 1.090 16.408 30648 Z= 0.409 Chirality : 0.038 0.199 3300 Planarity : 0.003 0.026 3372 Dihedral : 17.009 112.519 10560 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 3.06 (0.17), residues: 2364 helix: 3.00 (0.12), residues: 1704 sheet: 1.74 (0.44), residues: 132 loop : -1.46 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 4 HIS 0.002 0.001 HIS I 194 PHE 0.009 0.001 PHE B 32 TYR 0.008 0.001 TYR D 177 ARG 0.002 0.000 ARG F 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 467 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 455 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7802 (mtt90) REVERT: C 101 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7708 (mtp85) REVERT: F 101 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7761 (mtp85) outliers start: 12 outliers final: 0 residues processed: 455 average time/residue: 2.6919 time to fit residues: 1406.5258 Evaluate side-chains 330 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 3.407 ------------------------------------------------------------------------------- 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: 1.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN G 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23124 Z= 0.258 Angle : 0.687 7.793 30648 Z= 0.331 Chirality : 0.037 0.140 3300 Planarity : 0.005 0.047 3372 Dihedral : 15.881 139.530 6012 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.44 % Allowed : 10.56 % Favored : 88.01 % 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 (0.17), residues: 2364 helix: 2.97 (0.12), residues: 1692 sheet: 1.54 (0.43), residues: 132 loop : -1.23 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 4 HIS 0.003 0.001 HIS C 74 PHE 0.019 0.002 PHE B 52 TYR 0.015 0.002 TYR B 66 ARG 0.003 0.001 ARG J 189 *********************** 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 371 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 340 time to evaluate : 3.495 Fit side-chains revert: symmetry clash REVERT: E 9 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8762 (mtpp) REVERT: F 9 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8717 (mtpp) REVERT: H 213 MET cc_start: 0.9238 (mmm) cc_final: 0.8956 (mmm) outliers start: 31 outliers final: 11 residues processed: 357 average time/residue: 2.9069 time to fit residues: 1177.4637 Evaluate side-chains 344 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 333 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 148 optimal weight: 0.0570 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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: 0.8863 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 23124 Z= 0.137 Angle : 0.551 7.359 30648 Z= 0.264 Chirality : 0.034 0.108 3300 Planarity : 0.003 0.025 3372 Dihedral : 13.929 125.769 6012 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.44 % Allowed : 10.93 % Favored : 87.64 % 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: 3.31 (0.17), residues: 2364 helix: 3.14 (0.12), residues: 1716 sheet: 1.75 (0.45), residues: 132 loop : -1.26 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 25 HIS 0.002 0.001 HIS C 194 PHE 0.010 0.001 PHE C 97 TYR 0.007 0.001 TYR B 66 ARG 0.003 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 346 time to evaluate : 3.432 Fit side-chains REVERT: E 9 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8802 (mtpp) REVERT: H 213 MET cc_start: 0.9199 (mmm) cc_final: 0.8930 (mmm) outliers start: 31 outliers final: 17 residues processed: 363 average time/residue: 2.6278 time to fit residues: 1097.3392 Evaluate side-chains 345 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain L residue 3 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8903 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23124 Z= 0.210 Angle : 0.587 6.616 30648 Z= 0.293 Chirality : 0.037 0.149 3300 Planarity : 0.004 0.044 3372 Dihedral : 13.392 112.222 6012 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.39 % Allowed : 10.65 % Favored : 87.96 % 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: 3.14 (0.17), residues: 2364 helix: 3.00 (0.12), residues: 1716 sheet: 1.60 (0.44), residues: 132 loop : -1.22 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 45 HIS 0.002 0.001 HIS C 194 PHE 0.016 0.002 PHE L 199 TYR 0.012 0.002 TYR B 66 ARG 0.003 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 325 time to evaluate : 3.531 Fit side-chains REVERT: A 229 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7897 (t80) REVERT: D 153 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7958 (mtp-110) REVERT: H 213 MET cc_start: 0.9228 (mmm) cc_final: 0.8945 (mmm) outliers start: 30 outliers final: 18 residues processed: 342 average time/residue: 2.5827 time to fit residues: 1019.6374 Evaluate side-chains 341 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 322 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 157 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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: 0.8910 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23124 Z= 0.218 Angle : 0.589 5.877 30648 Z= 0.298 Chirality : 0.037 0.141 3300 Planarity : 0.005 0.045 3372 Dihedral : 13.194 86.930 6012 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.39 % Allowed : 10.79 % Favored : 87.82 % 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: 3.04 (0.17), residues: 2364 helix: 2.91 (0.12), residues: 1716 sheet: 1.66 (0.44), residues: 132 loop : -1.23 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 4 HIS 0.003 0.001 HIS J 74 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.002 TYR B 66 ARG 0.002 0.000 ARG K 189 *********************** 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 354 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 324 time to evaluate : 3.522 Fit side-chains REVERT: A 229 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7915 (t80) REVERT: D 153 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7939 (mtp-110) REVERT: H 213 MET cc_start: 0.9223 (mmm) cc_final: 0.8921 (mmm) REVERT: K 93 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8876 (mt) outliers start: 30 outliers final: 16 residues processed: 339 average time/residue: 2.6226 time to fit residues: 1024.3740 Evaluate side-chains 336 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 318 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU 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: 3.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 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: 0.8914 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23124 Z= 0.219 Angle : 0.582 5.832 30648 Z= 0.295 Chirality : 0.037 0.144 3300 Planarity : 0.004 0.044 3372 Dihedral : 12.986 85.613 6012 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.57 % Allowed : 11.25 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.17), residues: 2364 helix: 2.87 (0.12), residues: 1716 sheet: 1.66 (0.44), residues: 132 loop : -1.21 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 78 HIS 0.003 0.001 HIS G 74 PHE 0.016 0.002 PHE L 199 TYR 0.013 0.002 TYR B 66 ARG 0.004 0.000 ARG G 101 *********************** 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 348 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 314 time to evaluate : 3.417 Fit side-chains REVERT: A 229 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7926 (t80) REVERT: D 153 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7961 (mtp-110) REVERT: H 213 MET cc_start: 0.9220 (mmm) cc_final: 0.8908 (mmm) REVERT: K 93 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8871 (mt) outliers start: 34 outliers final: 24 residues processed: 335 average time/residue: 2.5388 time to fit residues: 984.0850 Evaluate side-chains 338 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 312 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.8901 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23124 Z= 0.177 Angle : 0.541 5.237 30648 Z= 0.274 Chirality : 0.035 0.127 3300 Planarity : 0.004 0.039 3372 Dihedral : 12.498 87.584 6012 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.44 % Allowed : 11.57 % Favored : 86.99 % 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: 3.11 (0.17), residues: 2364 helix: 2.96 (0.12), residues: 1716 sheet: 1.79 (0.45), residues: 132 loop : -1.21 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 45 HIS 0.002 0.001 HIS L 74 PHE 0.012 0.002 PHE E 199 TYR 0.010 0.001 TYR L 66 ARG 0.002 0.000 ARG I 101 *********************** 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 346 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 315 time to evaluate : 3.501 Fit side-chains REVERT: A 229 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7931 (t80) REVERT: D 153 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7916 (mtp-110) REVERT: H 213 MET cc_start: 0.9202 (mmm) cc_final: 0.8880 (mmm) REVERT: I 39 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8213 (p) REVERT: K 93 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8855 (mt) outliers start: 31 outliers final: 22 residues processed: 335 average time/residue: 2.5125 time to fit residues: 973.7574 Evaluate side-chains 338 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 313 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23124 Z= 0.250 Angle : 0.590 5.634 30648 Z= 0.301 Chirality : 0.038 0.145 3300 Planarity : 0.005 0.044 3372 Dihedral : 12.707 89.963 6012 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.53 % Allowed : 11.67 % Favored : 86.81 % 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: 2.94 (0.17), residues: 2364 helix: 2.83 (0.12), residues: 1716 sheet: 1.61 (0.44), residues: 132 loop : -1.23 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 45 HIS 0.003 0.001 HIS J 74 PHE 0.019 0.002 PHE F 199 TYR 0.014 0.002 TYR B 66 ARG 0.003 0.000 ARG C 189 *********************** 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 339 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 3.649 Fit side-chains REVERT: A 229 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7917 (t80) REVERT: D 153 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7983 (mtp-110) REVERT: H 213 MET cc_start: 0.9219 (mmm) cc_final: 0.8897 (mmm) REVERT: K 93 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8857 (mt) outliers start: 33 outliers final: 24 residues processed: 326 average time/residue: 2.5752 time to fit residues: 971.3698 Evaluate side-chains 333 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8906 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23124 Z= 0.178 Angle : 0.544 5.253 30648 Z= 0.277 Chirality : 0.035 0.123 3300 Planarity : 0.004 0.040 3372 Dihedral : 12.286 89.204 6012 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.48 % Allowed : 11.90 % Favored : 86.62 % 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: 3.07 (0.17), residues: 2364 helix: 2.93 (0.12), residues: 1716 sheet: 1.76 (0.45), residues: 132 loop : -1.22 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 25 HIS 0.002 0.001 HIS E 74 PHE 0.013 0.002 PHE L 199 TYR 0.011 0.001 TYR E 66 ARG 0.002 0.000 ARG I 101 *********************** 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 339 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 3.145 Fit side-chains REVERT: A 229 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7920 (t80) REVERT: K 93 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8831 (mt) outliers start: 32 outliers final: 26 residues processed: 326 average time/residue: 2.6248 time to fit residues: 985.3289 Evaluate side-chains 332 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 304 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 229 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 190 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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: 0.8927 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23124 Z= 0.269 Angle : 0.606 5.696 30648 Z= 0.310 Chirality : 0.038 0.147 3300 Planarity : 0.005 0.048 3372 Dihedral : 12.598 89.764 6012 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.62 % Allowed : 11.90 % Favored : 86.48 % 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: 2.83 (0.17), residues: 2364 helix: 2.83 (0.12), residues: 1704 sheet: 0.50 (0.35), residues: 204 loop : -1.44 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 78 HIS 0.003 0.001 HIS J 74 PHE 0.020 0.002 PHE F 199 TYR 0.016 0.002 TYR E 66 ARG 0.003 0.000 ARG A 76 ********************** 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 343 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 3.485 Fit side-chains REVERT: A 229 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7910 (t80) REVERT: H 213 MET cc_start: 0.9209 (mmm) cc_final: 0.8885 (mmm) REVERT: K 93 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8854 (mt) outliers start: 35 outliers final: 27 residues processed: 331 average time/residue: 2.6316 time to fit residues: 1005.2436 Evaluate side-chains 335 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 306 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091569 restraints weight = 68404.764| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.36 r_work: 0.2918 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23124 Z= 0.159 Angle : 0.526 5.208 30648 Z= 0.267 Chirality : 0.034 0.110 3300 Planarity : 0.004 0.035 3372 Dihedral : 11.891 89.883 6012 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.39 % Allowed : 12.22 % Favored : 86.39 % 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: 3.11 (0.17), residues: 2364 helix: 2.96 (0.12), residues: 1716 sheet: 1.83 (0.45), residues: 132 loop : -1.24 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 25 HIS 0.003 0.001 HIS I 74 PHE 0.011 0.001 PHE L 199 TYR 0.010 0.001 TYR E 66 ARG 0.001 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16557.42 seconds wall clock time: 290 minutes 47.96 seconds (17447.96 seconds total)