Starting phenix.real_space_refine on Sat Jul 4 15:14:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfu_27414/07_2026/8dfu_27414.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 60 5.16 5 C 15720 2.51 5 N 3180 2.21 5 O 3690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22710 Number of models: 1 Model: "" Number of chains: 56 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "A" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "D" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "E" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "F" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "G" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "J" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "K" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "L" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "M" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "N" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "O" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "P" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Q" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "R" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "S" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "T" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "V" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "W" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "X" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Y" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Z" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "0" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "1" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "2" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "3" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'RHR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'RHR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.37, per 1000 atoms: 0.15 Number of scatterers: 22710 At special positions: 0 Unit cell: (101.52, 101.52, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 60 15.00 O 3690 8.00 N 3180 7.00 C 15720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=81, symmetry=0 Number of additional bonds: simple=81, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 730.3 milliseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY B 36 " --> pdb=" O TRP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY G 36 " --> pdb=" O TRP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA G 70 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY H 36 " --> pdb=" O TRP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA H 70 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY I 36 " --> pdb=" O TRP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY J 36 " --> pdb=" O TRP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY K 36 " --> pdb=" O TRP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY L 36 " --> pdb=" O TRP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA L 70 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY M 36 " --> pdb=" O TRP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA M 63 " --> pdb=" O ALA M 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY N 36 " --> pdb=" O TRP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU N 64 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA N 70 " --> pdb=" O THR N 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY O 36 " --> pdb=" O TRP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA O 70 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY P 36 " --> pdb=" O TRP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA P 70 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY Q 36 " --> pdb=" O TRP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Q 70 " --> pdb=" O THR Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY S 36 " --> pdb=" O TRP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA S 63 " --> pdb=" O ALA S 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU S 64 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 37 removed outlier: 3.595A pdb=" N GLY T 36 " --> pdb=" O TRP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA T 63 " --> pdb=" O ALA T 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU T 64 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA T 70 " --> pdb=" O THR T 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY U 36 " --> pdb=" O TRP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA U 70 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY V 36 " --> pdb=" O TRP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA V 63 " --> pdb=" O ALA V 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU V 64 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA V 70 " --> pdb=" O THR V 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY W 36 " --> pdb=" O TRP W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU W 64 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA W 70 " --> pdb=" O THR W 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY X 36 " --> pdb=" O TRP X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 84 removed outlier: 4.695A pdb=" N ALA X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU X 64 " --> pdb=" O LEU X 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA X 70 " --> pdb=" O THR X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 37 removed outlier: 3.597A pdb=" N GLY Y 36 " --> pdb=" O TRP Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Y 64 " --> pdb=" O LEU Y 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Y 70 " --> pdb=" O THR Y 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY Z 36 " --> pdb=" O TRP Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Z 64 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Z 70 " --> pdb=" O THR Z 66 " (cutoff:3.500A) Processing helix chain '0' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY 0 36 " --> pdb=" O TRP 0 32 " (cutoff:3.500A) Processing helix chain '0' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA 0 63 " --> pdb=" O ALA 0 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 0 64 " --> pdb=" O LEU 0 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 0 70 " --> pdb=" O THR 0 66 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY 1 36 " --> pdb=" O TRP 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA 1 63 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 1 64 " --> pdb=" O LEU 1 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 1 70 " --> pdb=" O THR 1 66 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY 2 36 " --> pdb=" O TRP 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA 2 63 " --> pdb=" O ALA 2 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 2 64 " --> pdb=" O LEU 2 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA 2 70 " --> pdb=" O THR 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 37 removed outlier: 3.596A pdb=" N GLY 3 36 " --> pdb=" O TRP 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 84 removed outlier: 4.694A pdb=" N ALA 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 3 64 " --> pdb=" O LEU 3 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 3 70 " --> pdb=" O THR 3 66 " (cutoff:3.500A) 1980 hydrogen bonds defined for protein. 5940 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: 3.77 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5910 1.34 - 1.45: 2807 1.45 - 1.57: 14143 1.57 - 1.68: 60 1.68 - 1.80: 120 Bond restraints: 23040 Sorted by residual: bond pdb=" O03 RHR C 203 " pdb=" P02 RHR C 203 " ideal model delta sigma weight residual 1.713 1.657 0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" O03 RHR W 201 " pdb=" P02 RHR W 201 " ideal model delta sigma weight residual 1.713 1.657 0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" O03 RHR L 201 " pdb=" P02 RHR L 201 " ideal model delta sigma weight residual 1.713 1.657 0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" O03 RHR C 201 " pdb=" P02 RHR C 201 " ideal model delta sigma weight residual 1.713 1.657 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" O03 RHR Z 201 " pdb=" P02 RHR Z 201 " ideal model delta sigma weight residual 1.713 1.657 0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 23035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 28325 1.80 - 3.60: 1773 3.60 - 5.41: 682 5.41 - 7.21: 150 7.21 - 9.01: 60 Bond angle restraints: 30990 Sorted by residual: angle pdb=" O03 RHR W 201 " pdb=" P02 RHR W 201 " pdb=" O59 RHR W 201 " ideal model delta sigma weight residual 100.53 109.54 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" O03 RHR K 201 " pdb=" P02 RHR K 201 " pdb=" O59 RHR K 201 " ideal model delta sigma weight residual 100.53 109.54 -9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" O03 RHR A 102 " pdb=" P02 RHR A 102 " pdb=" O59 RHR A 102 " ideal model delta sigma weight residual 100.53 109.54 -9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" O03 RHR H 201 " pdb=" P02 RHR H 201 " pdb=" O59 RHR H 201 " ideal model delta sigma weight residual 100.53 109.52 -8.99 3.00e+00 1.11e-01 8.97e+00 angle pdb=" O03 RHR F 202 " pdb=" P02 RHR F 202 " pdb=" O59 RHR F 202 " ideal model delta sigma weight residual 100.53 109.51 -8.98 3.00e+00 1.11e-01 8.96e+00 ... (remaining 30985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 13065 33.94 - 67.88: 1605 67.88 - 101.83: 300 101.83 - 135.77: 120 135.77 - 169.71: 120 Dihedral angle restraints: 15210 sinusoidal: 8100 harmonic: 7110 Sorted by residual: dihedral pdb=" C51 RHR O 202 " pdb=" C50 RHR O 202 " pdb=" C52 RHR O 202 " pdb=" C53 RHR O 202 " ideal model delta sinusoidal sigma weight residual 57.36 -112.35 169.71 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C51 RHR C 202 " pdb=" C50 RHR C 202 " pdb=" C52 RHR C 202 " pdb=" C53 RHR C 202 " ideal model delta sinusoidal sigma weight residual 57.36 -112.33 169.69 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C51 RHR G 202 " pdb=" C50 RHR G 202 " pdb=" C52 RHR G 202 " pdb=" C53 RHR G 202 " ideal model delta sinusoidal sigma weight residual 57.36 -112.33 169.69 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 15207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.076: 3690 1.076 - 2.152: 0 2.152 - 3.228: 0 3.228 - 4.304: 0 4.304 - 5.380: 180 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C45 RHR K 202 " pdb=" C44 RHR K 202 " pdb=" C46 RHR K 202 " pdb=" C47 RHR K 202 " both_signs ideal model delta sigma weight residual False -2.66 2.72 -5.38 2.00e-01 2.50e+01 7.24e+02 chirality pdb=" C45 RHR A 101 " pdb=" C44 RHR A 101 " pdb=" C46 RHR A 101 " pdb=" C47 RHR A 101 " both_signs ideal model delta sigma weight residual False -2.66 2.71 -5.38 2.00e-01 2.50e+01 7.24e+02 chirality pdb=" C45 RHR T 202 " pdb=" C44 RHR T 202 " pdb=" C46 RHR T 202 " pdb=" C47 RHR T 202 " both_signs ideal model delta sigma weight residual False -2.66 2.71 -5.38 2.00e-01 2.50e+01 7.23e+02 ... (remaining 3867 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 69 " 0.011 2.00e-02 2.50e+03 8.49e-03 1.26e+00 pdb=" CG PHE R 69 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 69 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE R 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 69 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 69 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 69 " -0.011 2.00e-02 2.50e+03 8.48e-03 1.26e+00 pdb=" CG PHE 3 69 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 69 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 3 69 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 69 " 0.011 2.00e-02 2.50e+03 8.47e-03 1.26e+00 pdb=" CG PHE O 69 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE O 69 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE O 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE O 69 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE O 69 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE O 69 " 0.003 2.00e-02 2.50e+03 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 9860 2.95 - 3.44: 22771 3.44 - 3.92: 35580 3.92 - 4.41: 40049 4.41 - 4.90: 63109 Nonbonded interactions: 171369 Sorted by model distance: nonbonded pdb=" N ASP F 4 " pdb=" OD1 ASP F 4 " model vdw 2.461 3.120 nonbonded pdb=" N ASP A 4 " pdb=" OD1 ASP A 4 " model vdw 2.461 3.120 nonbonded pdb=" N ASP S 4 " pdb=" OD1 ASP S 4 " model vdw 2.462 3.120 nonbonded pdb=" N ASP J 4 " pdb=" OD1 ASP J 4 " model vdw 2.462 3.120 nonbonded pdb=" N ASP 0 4 " pdb=" OD1 ASP 0 4 " model vdw 2.462 3.120 ... (remaining 171364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.110 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.013 0.276 23121 Z= 0.798 Angle : 1.196 9.009 30990 Z= 0.487 Chirality : 1.138 5.380 3870 Planarity : 0.004 0.025 3150 Dihedral : 33.961 169.711 10590 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2460 helix: 0.84 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 35 PHE 0.019 0.003 PHE R 69 TRP 0.013 0.002 TRP 0 28 Details of bonding type rmsd/Z covalent geometry : bond 0.01200 / 0.58 (23040) covalent geometry : angle 1.19608 / 0.49 (30990) hydrogen bonds : bond 0.10194 / 6.85 ( 1980) hydrogen bonds : angle 4.24575 / 3.18 ( 5940) Misc. bond : bond 0.09314 / 5.64 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8014 (tt0) cc_final: 0.7518 (tt0) REVERT: A 53 GLU cc_start: 0.7695 (tt0) cc_final: 0.7482 (tt0) REVERT: A 54 ASP cc_start: 0.8369 (m-30) cc_final: 0.7990 (m-30) REVERT: A 81 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 81 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 53 GLU cc_start: 0.7935 (tt0) cc_final: 0.7408 (tt0) REVERT: D 81 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 35 ARG cc_start: 0.9000 (ttt90) cc_final: 0.8795 (mtp180) REVERT: E 53 GLU cc_start: 0.7956 (tt0) cc_final: 0.7646 (tt0) REVERT: F 53 GLU cc_start: 0.7869 (tt0) cc_final: 0.7443 (tt0) REVERT: H 81 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8423 (tm-30) REVERT: I 7 GLN cc_start: 0.8305 (tp40) cc_final: 0.7634 (tp40) REVERT: I 11 ASP cc_start: 0.8669 (m-30) cc_final: 0.8143 (m-30) REVERT: I 53 GLU cc_start: 0.7914 (tt0) cc_final: 0.7406 (tt0) REVERT: I 81 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8375 (tm-30) REVERT: J 53 GLU cc_start: 0.7871 (tt0) cc_final: 0.7644 (tt0) REVERT: K 53 GLU cc_start: 0.7964 (tt0) cc_final: 0.7527 (tt0) REVERT: K 81 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8475 (tm-30) REVERT: L 53 GLU cc_start: 0.7906 (tt0) cc_final: 0.7386 (tt0) REVERT: M 53 GLU cc_start: 0.7943 (tt0) cc_final: 0.7419 (tt0) REVERT: N 53 GLU cc_start: 0.7740 (tt0) cc_final: 0.7210 (tt0) REVERT: N 81 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8487 (tm-30) REVERT: P 53 GLU cc_start: 0.7838 (tt0) cc_final: 0.7575 (tt0) REVERT: P 81 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8491 (tm-30) REVERT: Q 7 GLN cc_start: 0.8222 (tp40) cc_final: 0.7830 (tp40) REVERT: Q 11 ASP cc_start: 0.8783 (m-30) cc_final: 0.8502 (m-30) REVERT: Q 53 GLU cc_start: 0.8037 (tt0) cc_final: 0.7619 (tt0) REVERT: R 53 GLU cc_start: 0.7947 (tt0) cc_final: 0.7531 (tt0) REVERT: S 53 GLU cc_start: 0.7889 (tt0) cc_final: 0.7501 (tt0) REVERT: S 81 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8444 (tm-30) REVERT: T 7 GLN cc_start: 0.8268 (tp40) cc_final: 0.7769 (tp40) REVERT: T 11 ASP cc_start: 0.8515 (m-30) cc_final: 0.8167 (m-30) REVERT: T 53 GLU cc_start: 0.7896 (tt0) cc_final: 0.7455 (tt0) REVERT: T 81 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8362 (tm-30) REVERT: U 53 GLU cc_start: 0.7753 (tt0) cc_final: 0.7484 (tt0) REVERT: U 81 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8417 (tm-30) REVERT: V 53 GLU cc_start: 0.7930 (tt0) cc_final: 0.7621 (tt0) REVERT: V 81 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8391 (tm-30) REVERT: W 53 GLU cc_start: 0.7842 (tt0) cc_final: 0.7377 (tt0) REVERT: X 81 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8531 (tm-30) REVERT: Y 53 GLU cc_start: 0.7868 (tt0) cc_final: 0.7391 (tt0) REVERT: Z 53 GLU cc_start: 0.8028 (tt0) cc_final: 0.7657 (tt0) REVERT: 0 35 ARG cc_start: 0.9028 (ttt90) cc_final: 0.8817 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7849 (tt0) cc_final: 0.7603 (tt0) REVERT: 0 74 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7796 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8456 (tm-30) REVERT: 1 53 GLU cc_start: 0.7852 (tt0) cc_final: 0.7411 (tt0) REVERT: 1 74 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7836 (ttp-170) REVERT: 1 81 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8450 (tm-30) REVERT: 2 53 GLU cc_start: 0.7707 (tt0) cc_final: 0.7450 (tt0) REVERT: 2 74 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7740 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8384 (tm-30) REVERT: 3 37 SER cc_start: 0.9256 (m) cc_final: 0.9017 (m) REVERT: 3 74 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7741 (ttp-170) REVERT: 3 81 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8474 (tm-30) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.2051 time to fit residues: 119.9965 Evaluate side-chains 346 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088090 restraints weight = 35983.628| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.58 r_work: 0.2911 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23121 Z= 0.140 Angle : 0.483 4.314 30990 Z= 0.248 Chirality : 0.033 0.115 3870 Planarity : 0.004 0.028 3150 Dihedral : 32.515 160.539 6570 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.70 % Allowed : 11.79 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.17), residues: 2460 helix: 2.13 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 1.25 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 46 PHE 0.004 0.001 PHE C 69 TRP 0.011 0.001 TRP 2 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (23040) covalent geometry : angle 0.48318 / 0.25 (30990) hydrogen bonds : bond 0.05761 / 3.93 ( 1980) hydrogen bonds : angle 3.52357 / 2.64 ( 5940) Misc. bond : bond 0.00060 / 0.04 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 360 time to evaluate : 0.605 Fit side-chains REVERT: A 35 ARG cc_start: 0.8974 (ttt-90) cc_final: 0.8608 (mtp85) REVERT: A 54 ASP cc_start: 0.8662 (m-30) cc_final: 0.8329 (m-30) REVERT: A 81 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 81 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8639 (tm-30) REVERT: D 11 ASP cc_start: 0.8660 (m-30) cc_final: 0.8249 (m-30) REVERT: D 53 GLU cc_start: 0.8340 (tt0) cc_final: 0.7817 (tt0) REVERT: E 81 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8603 (tm-30) REVERT: F 53 GLU cc_start: 0.8426 (tt0) cc_final: 0.8103 (tt0) REVERT: H 81 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8526 (tm-30) REVERT: I 53 GLU cc_start: 0.8315 (tt0) cc_final: 0.7809 (tt0) REVERT: I 81 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8585 (tm-30) REVERT: J 53 GLU cc_start: 0.8334 (tt0) cc_final: 0.8080 (tt0) REVERT: K 53 GLU cc_start: 0.8522 (tt0) cc_final: 0.8071 (tt0) REVERT: K 81 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8697 (tm-30) REVERT: M 53 GLU cc_start: 0.8445 (tt0) cc_final: 0.8074 (tt0) REVERT: N 81 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8762 (tm-30) REVERT: P 53 GLU cc_start: 0.8386 (tt0) cc_final: 0.8099 (tt0) REVERT: P 81 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8579 (tm-30) REVERT: Q 53 GLU cc_start: 0.8349 (tt0) cc_final: 0.7947 (tt0) REVERT: S 53 GLU cc_start: 0.8348 (tt0) cc_final: 0.8004 (tt0) REVERT: T 35 ARG cc_start: 0.9060 (ttt90) cc_final: 0.8763 (mtp180) REVERT: T 53 GLU cc_start: 0.8303 (tt0) cc_final: 0.7824 (tt0) REVERT: T 81 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8697 (tm-30) REVERT: U 16 LEU cc_start: 0.8983 (tp) cc_final: 0.8777 (tp) REVERT: U 46 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8124 (mtm110) REVERT: U 53 GLU cc_start: 0.8189 (tt0) cc_final: 0.7828 (tt0) REVERT: U 81 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8627 (tm-30) REVERT: V 53 GLU cc_start: 0.8319 (tt0) cc_final: 0.7957 (tt0) REVERT: V 81 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8636 (tm-30) REVERT: W 46 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8372 (mtm110) REVERT: W 53 GLU cc_start: 0.8307 (tt0) cc_final: 0.7830 (tt0) REVERT: X 81 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8656 (tm-30) REVERT: Y 53 GLU cc_start: 0.8384 (tt0) cc_final: 0.7933 (tt0) REVERT: 0 35 ARG cc_start: 0.9022 (ttt90) cc_final: 0.8711 (ttt-90) REVERT: 0 53 GLU cc_start: 0.8261 (tt0) cc_final: 0.8010 (tt0) REVERT: 0 74 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.7869 (ttp-170) REVERT: 1 53 GLU cc_start: 0.8231 (tt0) cc_final: 0.7830 (tt0) REVERT: 1 74 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.7859 (ttp80) REVERT: 1 81 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8629 (tm-30) REVERT: 2 53 GLU cc_start: 0.8347 (tt0) cc_final: 0.7991 (tt0) REVERT: 2 74 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.7873 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8646 (tm-30) REVERT: 3 53 GLU cc_start: 0.8310 (tt0) cc_final: 0.8042 (tt0) REVERT: 3 81 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8645 (tm-30) outliers start: 14 outliers final: 7 residues processed: 364 average time/residue: 0.1460 time to fit residues: 84.0918 Evaluate side-chains 325 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 318 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain 2 residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.080510 restraints weight = 36161.335| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.59 r_work: 0.2776 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23121 Z= 0.209 Angle : 0.569 6.257 30990 Z= 0.288 Chirality : 0.036 0.105 3870 Planarity : 0.004 0.034 3150 Dihedral : 29.321 156.699 6570 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.04 % Allowed : 14.98 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.16), residues: 2460 helix: 2.47 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.14 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 74 PHE 0.019 0.003 PHE V 69 TRP 0.015 0.002 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (23040) covalent geometry : angle 0.56916 / 0.29 (30990) hydrogen bonds : bond 0.07509 / 5.13 ( 1980) hydrogen bonds : angle 3.86544 / 2.89 ( 5940) Misc. bond : bond 0.00080 / 0.06 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8497 (tt0) cc_final: 0.7981 (tt0) REVERT: A 46 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.8190 (mtm110) REVERT: A 54 ASP cc_start: 0.8775 (m-30) cc_final: 0.8475 (m-30) REVERT: A 81 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 81 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8630 (tm-30) REVERT: D 7 GLN cc_start: 0.8371 (tp40) cc_final: 0.8112 (tp40) REVERT: D 53 GLU cc_start: 0.8490 (tt0) cc_final: 0.7917 (tt0) REVERT: E 53 GLU cc_start: 0.8459 (tt0) cc_final: 0.8005 (tt0) REVERT: E 81 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8613 (tm-30) REVERT: F 53 GLU cc_start: 0.8511 (tt0) cc_final: 0.8064 (tt0) REVERT: H 7 GLN cc_start: 0.8389 (tp40) cc_final: 0.8128 (tp40) REVERT: H 81 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8542 (tm-30) REVERT: I 11 ASP cc_start: 0.8939 (m-30) cc_final: 0.8420 (m-30) REVERT: I 53 GLU cc_start: 0.8483 (tt0) cc_final: 0.7981 (tt0) REVERT: I 81 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8578 (tm-30) REVERT: J 53 GLU cc_start: 0.8491 (tt0) cc_final: 0.8126 (tt0) REVERT: K 53 GLU cc_start: 0.8515 (tt0) cc_final: 0.7996 (tt0) REVERT: K 81 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8704 (tm-30) REVERT: L 53 GLU cc_start: 0.8543 (tt0) cc_final: 0.7955 (tt0) REVERT: M 53 GLU cc_start: 0.8562 (tt0) cc_final: 0.8164 (tt0) REVERT: N 11 ASP cc_start: 0.8683 (m-30) cc_final: 0.8411 (m-30) REVERT: N 53 GLU cc_start: 0.8340 (tt0) cc_final: 0.7862 (tt0) REVERT: N 81 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8793 (tm-30) REVERT: P 53 GLU cc_start: 0.8495 (tt0) cc_final: 0.8098 (tt0) REVERT: P 81 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8621 (tm-30) REVERT: Q 7 GLN cc_start: 0.8273 (tp40) cc_final: 0.7848 (tp40) REVERT: Q 11 ASP cc_start: 0.8975 (m-30) cc_final: 0.8701 (m-30) REVERT: Q 53 GLU cc_start: 0.8491 (tt0) cc_final: 0.7991 (tt0) REVERT: R 46 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8361 (mtp-110) REVERT: R 53 GLU cc_start: 0.8496 (tt0) cc_final: 0.7878 (tt0) REVERT: S 53 GLU cc_start: 0.8519 (tt0) cc_final: 0.8126 (tt0) REVERT: T 35 ARG cc_start: 0.9092 (ttt90) cc_final: 0.8813 (mtp180) REVERT: T 53 GLU cc_start: 0.8417 (tt0) cc_final: 0.7931 (tt0) REVERT: T 81 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8759 (tm-30) REVERT: U 53 GLU cc_start: 0.8303 (tt0) cc_final: 0.7939 (tt0) REVERT: U 81 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8723 (tm-30) REVERT: V 46 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8539 (mtm110) REVERT: V 53 GLU cc_start: 0.8459 (tt0) cc_final: 0.8052 (tt0) REVERT: V 81 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8599 (tm-30) REVERT: W 53 GLU cc_start: 0.8486 (tt0) cc_final: 0.7991 (tt0) REVERT: X 81 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8644 (tm-30) REVERT: Y 53 GLU cc_start: 0.8436 (tt0) cc_final: 0.7911 (tt0) REVERT: Z 53 GLU cc_start: 0.8643 (tt0) cc_final: 0.8119 (tt0) REVERT: 0 53 GLU cc_start: 0.8400 (tt0) cc_final: 0.8080 (tt0) REVERT: 0 74 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.7919 (ttp-170) REVERT: 0 81 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8718 (tm-30) REVERT: 1 11 ASP cc_start: 0.8739 (m-30) cc_final: 0.8418 (m-30) REVERT: 1 53 GLU cc_start: 0.8377 (tt0) cc_final: 0.7874 (tt0) REVERT: 1 74 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.7909 (ttp-170) REVERT: 1 81 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8687 (tm-30) REVERT: 2 53 GLU cc_start: 0.8448 (tt0) cc_final: 0.7890 (tt0) REVERT: 2 74 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.7860 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8673 (tm-30) REVERT: 3 53 GLU cc_start: 0.8359 (tt0) cc_final: 0.8065 (tt0) REVERT: 3 81 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8755 (tm-30) outliers start: 41 outliers final: 32 residues processed: 362 average time/residue: 0.1773 time to fit residues: 94.2835 Evaluate side-chains 366 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 334 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 41 SER Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 2 residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090113 restraints weight = 35612.243| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.58 r_work: 0.2937 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23121 Z= 0.133 Angle : 0.468 6.839 30990 Z= 0.244 Chirality : 0.033 0.141 3870 Planarity : 0.004 0.027 3150 Dihedral : 26.021 155.350 6570 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.14 % Allowed : 17.01 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.17), residues: 2460 helix: 2.86 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.19 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 35 PHE 0.005 0.001 PHE D 69 TRP 0.012 0.001 TRP 0 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (23040) covalent geometry : angle 0.46769 / 0.24 (30990) hydrogen bonds : bond 0.05367 / 3.66 ( 1980) hydrogen bonds : angle 3.41704 / 2.55 ( 5940) Misc. bond : bond 0.00161 / 0.11 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 337 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8612 (m-30) cc_final: 0.8243 (m-30) REVERT: A 81 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8601 (tm-30) REVERT: C 81 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8464 (tm-30) REVERT: D 53 GLU cc_start: 0.8361 (tt0) cc_final: 0.7800 (tt0) REVERT: E 81 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8642 (tm-30) REVERT: F 53 GLU cc_start: 0.8404 (tt0) cc_final: 0.8022 (tt0) REVERT: H 81 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8544 (tm-30) REVERT: I 53 GLU cc_start: 0.8374 (tt0) cc_final: 0.7888 (tt0) REVERT: J 53 GLU cc_start: 0.8360 (tt0) cc_final: 0.7985 (tt0) REVERT: K 53 GLU cc_start: 0.8504 (tt0) cc_final: 0.8044 (tt0) REVERT: K 81 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8659 (tm-30) REVERT: M 53 GLU cc_start: 0.8471 (tt0) cc_final: 0.7898 (tt0) REVERT: N 81 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8769 (tm-30) REVERT: P 53 GLU cc_start: 0.8422 (tt0) cc_final: 0.7943 (tt0) REVERT: P 81 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8579 (tm-30) REVERT: Q 53 GLU cc_start: 0.8296 (tt0) cc_final: 0.7902 (tt0) REVERT: R 81 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8716 (tm-30) REVERT: S 53 GLU cc_start: 0.8434 (tt0) cc_final: 0.8073 (tt0) REVERT: T 35 ARG cc_start: 0.9015 (ttt90) cc_final: 0.8727 (mmm160) REVERT: T 53 GLU cc_start: 0.8225 (tt0) cc_final: 0.7734 (tt0) REVERT: T 81 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8734 (tm-30) REVERT: U 53 GLU cc_start: 0.8206 (tt0) cc_final: 0.7815 (tt0) REVERT: U 81 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8607 (tm-30) REVERT: V 53 GLU cc_start: 0.8311 (tt0) cc_final: 0.7926 (tt0) REVERT: V 81 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8521 (tm-30) REVERT: W 53 GLU cc_start: 0.8314 (tt0) cc_final: 0.7770 (tt0) REVERT: X 81 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8758 (tm-30) REVERT: Y 53 GLU cc_start: 0.8386 (tt0) cc_final: 0.7918 (tt0) REVERT: 0 53 GLU cc_start: 0.8278 (tt0) cc_final: 0.7932 (tt0) REVERT: 0 74 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.7885 (ttp-170) REVERT: 1 74 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.7867 (ttp80) REVERT: 1 81 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8573 (tm-30) REVERT: 2 53 GLU cc_start: 0.8347 (tt0) cc_final: 0.7749 (tt0) REVERT: 2 74 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.7875 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8627 (tm-30) REVERT: 3 81 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8643 (tm-30) outliers start: 23 outliers final: 9 residues processed: 353 average time/residue: 0.1374 time to fit residues: 77.2730 Evaluate side-chains 318 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 309 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 1 residue 68 VAL Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089538 restraints weight = 35030.155| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.56 r_work: 0.2923 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23121 Z= 0.136 Angle : 0.473 5.170 30990 Z= 0.248 Chirality : 0.033 0.166 3870 Planarity : 0.004 0.041 3150 Dihedral : 24.165 161.348 6570 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.69 % Allowed : 16.22 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.17), residues: 2460 helix: 3.03 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.82 (0.70), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 74 PHE 0.008 0.001 PHE Q 69 TRP 0.012 0.001 TRP 3 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (23040) covalent geometry : angle 0.47293 / 0.25 (30990) hydrogen bonds : bond 0.05650 / 3.86 ( 1980) hydrogen bonds : angle 3.41518 / 2.56 ( 5940) Misc. bond : bond 0.00156 / 0.11 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8878 (ttt-90) cc_final: 0.8441 (mtp85) REVERT: A 54 ASP cc_start: 0.8620 (m-30) cc_final: 0.8243 (m-30) REVERT: A 81 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 81 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 53 GLU cc_start: 0.8339 (tt0) cc_final: 0.7778 (tt0) REVERT: E 81 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8678 (tm-30) REVERT: F 53 GLU cc_start: 0.8372 (tt0) cc_final: 0.8016 (tt0) REVERT: H 81 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8586 (tm-30) REVERT: I 53 GLU cc_start: 0.8345 (tt0) cc_final: 0.7861 (tt0) REVERT: I 81 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8609 (tm-30) REVERT: J 53 GLU cc_start: 0.8369 (tt0) cc_final: 0.8082 (tt0) REVERT: K 53 GLU cc_start: 0.8495 (tt0) cc_final: 0.8052 (tt0) REVERT: K 81 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8667 (tm-30) REVERT: M 53 GLU cc_start: 0.8483 (tt0) cc_final: 0.8068 (tt0) REVERT: N 81 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8753 (tm-30) REVERT: O 81 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8692 (tm-30) REVERT: P 53 GLU cc_start: 0.8398 (tt0) cc_final: 0.7921 (tt0) REVERT: P 81 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8601 (tm-30) REVERT: Q 53 GLU cc_start: 0.8296 (tt0) cc_final: 0.7905 (tt0) REVERT: R 81 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8640 (tm-30) REVERT: T 35 ARG cc_start: 0.8963 (ttt90) cc_final: 0.8692 (mmm160) REVERT: T 53 GLU cc_start: 0.8249 (tt0) cc_final: 0.7753 (tt0) REVERT: T 81 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8832 (tm-30) REVERT: U 53 GLU cc_start: 0.8233 (tt0) cc_final: 0.7831 (tt0) REVERT: U 81 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8704 (tm-30) REVERT: V 53 GLU cc_start: 0.8288 (tt0) cc_final: 0.7894 (tt0) REVERT: V 81 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8522 (tm-30) REVERT: W 53 GLU cc_start: 0.8282 (tt0) cc_final: 0.7740 (tt0) REVERT: X 81 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8715 (tm-30) REVERT: Y 53 GLU cc_start: 0.8357 (tt0) cc_final: 0.7900 (tt0) REVERT: 0 53 GLU cc_start: 0.8294 (tt0) cc_final: 0.7824 (tt0) REVERT: 0 74 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.7887 (ttp-170) REVERT: 0 81 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8689 (tm-30) REVERT: 1 74 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.7896 (ttp-170) REVERT: 1 81 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8630 (tm-30) REVERT: 2 53 GLU cc_start: 0.8336 (tt0) cc_final: 0.7729 (tt0) REVERT: 2 74 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.7914 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8606 (tm-30) REVERT: 3 81 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8717 (tm-30) outliers start: 54 outliers final: 20 residues processed: 352 average time/residue: 0.1368 time to fit residues: 76.4538 Evaluate side-chains 326 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 306 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091783 restraints weight = 35367.156| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.56 r_work: 0.2960 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23121 Z= 0.135 Angle : 0.470 4.516 30990 Z= 0.252 Chirality : 0.035 0.226 3870 Planarity : 0.004 0.035 3150 Dihedral : 22.972 154.522 6570 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.24 % Allowed : 16.92 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.70 (0.17), residues: 2460 helix: 3.08 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.89 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 35 PHE 0.006 0.001 PHE M 69 TRP 0.012 0.001 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (23040) covalent geometry : angle 0.47019 / 0.25 (30990) hydrogen bonds : bond 0.05636 / 3.85 ( 1980) hydrogen bonds : angle 3.34842 / 2.52 ( 5940) Misc. bond : bond 0.00149 / 0.10 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8635 (m-30) cc_final: 0.8295 (m-30) REVERT: A 81 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8693 (tm-30) REVERT: C 81 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8463 (tm-30) REVERT: D 53 GLU cc_start: 0.8412 (tt0) cc_final: 0.7824 (tt0) REVERT: E 81 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 53 GLU cc_start: 0.8413 (tt0) cc_final: 0.8073 (tt0) REVERT: H 81 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8604 (tm-30) REVERT: I 53 GLU cc_start: 0.8338 (tt0) cc_final: 0.7833 (tt0) REVERT: I 81 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8592 (tm-30) REVERT: J 53 GLU cc_start: 0.8382 (tt0) cc_final: 0.7977 (tt0) REVERT: J 81 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8647 (tm-30) REVERT: K 53 GLU cc_start: 0.8524 (tt0) cc_final: 0.8101 (tt0) REVERT: K 81 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8657 (tm-30) REVERT: M 53 GLU cc_start: 0.8484 (tt0) cc_final: 0.8061 (tt0) REVERT: N 81 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8765 (tm-30) REVERT: O 81 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8709 (tm-30) REVERT: P 81 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8600 (tm-30) REVERT: Q 53 GLU cc_start: 0.8306 (tt0) cc_final: 0.7906 (tt0) REVERT: T 35 ARG cc_start: 0.8992 (ttt90) cc_final: 0.8731 (mmm160) REVERT: T 81 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8846 (tm-30) REVERT: U 53 GLU cc_start: 0.8246 (tt0) cc_final: 0.7831 (tt0) REVERT: U 81 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8705 (tm-30) REVERT: V 53 GLU cc_start: 0.8306 (tt0) cc_final: 0.7882 (tt0) REVERT: V 81 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8538 (tm-30) REVERT: W 53 GLU cc_start: 0.8296 (tt0) cc_final: 0.7749 (tt0) REVERT: Y 53 GLU cc_start: 0.8361 (tt0) cc_final: 0.7932 (tt0) REVERT: 0 53 GLU cc_start: 0.8296 (tt0) cc_final: 0.7842 (tt0) REVERT: 0 74 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.7946 (ttp80) REVERT: 0 81 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8695 (tm-30) REVERT: 1 74 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.7970 (ttp-170) REVERT: 1 81 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8623 (tm-30) REVERT: 2 53 GLU cc_start: 0.8359 (tt0) cc_final: 0.7759 (tt0) REVERT: 2 74 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.7935 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8659 (tm-30) REVERT: 3 81 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8737 (tm-30) outliers start: 25 outliers final: 12 residues processed: 319 average time/residue: 0.1412 time to fit residues: 72.0197 Evaluate side-chains 311 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 299 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 229 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088848 restraints weight = 35354.366| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.61 r_work: 0.2915 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23121 Z= 0.146 Angle : 0.484 4.967 30990 Z= 0.259 Chirality : 0.036 0.213 3870 Planarity : 0.004 0.041 3150 Dihedral : 22.686 153.297 6570 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.19 % Allowed : 17.11 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.67 (0.17), residues: 2460 helix: 3.05 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 3.08 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 74 PHE 0.010 0.001 PHE W 69 TRP 0.013 0.001 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (23040) covalent geometry : angle 0.48409 / 0.26 (30990) hydrogen bonds : bond 0.05979 / 4.09 ( 1980) hydrogen bonds : angle 3.43074 / 2.58 ( 5940) Misc. bond : bond 0.00159 / 0.11 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8614 (m-30) cc_final: 0.8279 (m-30) REVERT: A 81 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 81 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 11 ASP cc_start: 0.8706 (m-30) cc_final: 0.8243 (m-30) REVERT: D 53 GLU cc_start: 0.8389 (tt0) cc_final: 0.7826 (tt0) REVERT: E 81 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8731 (tm-30) REVERT: F 53 GLU cc_start: 0.8415 (tt0) cc_final: 0.8047 (tt0) REVERT: G 53 GLU cc_start: 0.8040 (tt0) cc_final: 0.7682 (tt0) REVERT: H 81 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8585 (tm-30) REVERT: I 53 GLU cc_start: 0.8331 (tt0) cc_final: 0.7820 (tt0) REVERT: I 81 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8617 (tm-30) REVERT: J 53 GLU cc_start: 0.8400 (tt0) cc_final: 0.8098 (tt0) REVERT: K 53 GLU cc_start: 0.8466 (tt0) cc_final: 0.8007 (tt0) REVERT: K 81 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8663 (tm-30) REVERT: M 53 GLU cc_start: 0.8529 (tt0) cc_final: 0.8100 (tt0) REVERT: N 81 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8748 (tm-30) REVERT: O 81 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8770 (tm-30) REVERT: P 53 GLU cc_start: 0.8450 (tt0) cc_final: 0.7948 (tt0) REVERT: P 81 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8591 (tm-30) REVERT: Q 53 GLU cc_start: 0.8286 (tt0) cc_final: 0.7877 (tt0) REVERT: T 35 ARG cc_start: 0.9032 (ttt90) cc_final: 0.8745 (mmm160) REVERT: T 53 GLU cc_start: 0.8274 (tt0) cc_final: 0.7813 (tt0) REVERT: T 81 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8801 (tm-30) REVERT: U 53 GLU cc_start: 0.8236 (tt0) cc_final: 0.7892 (tt0) REVERT: U 81 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8748 (tm-30) REVERT: V 53 GLU cc_start: 0.8328 (tt0) cc_final: 0.7879 (tt0) REVERT: V 81 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8552 (tm-30) REVERT: W 53 GLU cc_start: 0.8321 (tt0) cc_final: 0.7763 (tt0) REVERT: X 81 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8654 (tm-30) REVERT: Y 53 GLU cc_start: 0.8376 (tt0) cc_final: 0.7934 (tt0) REVERT: 0 53 GLU cc_start: 0.8329 (tt0) cc_final: 0.7968 (tt0) REVERT: 0 74 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.7951 (ttp80) REVERT: 0 81 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8750 (tm-30) REVERT: 1 53 GLU cc_start: 0.8288 (tt0) cc_final: 0.7798 (tt0) REVERT: 1 74 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.7865 (ttp80) REVERT: 1 81 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8653 (tm-30) REVERT: 2 53 GLU cc_start: 0.8373 (tt0) cc_final: 0.7764 (tt0) REVERT: 2 74 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.7893 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8705 (tm-30) REVERT: 3 81 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8755 (tm-30) outliers start: 24 outliers final: 18 residues processed: 317 average time/residue: 0.1377 time to fit residues: 69.3108 Evaluate side-chains 316 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088694 restraints weight = 35049.033| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.55 r_work: 0.2909 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23121 Z= 0.153 Angle : 0.497 5.644 30990 Z= 0.265 Chirality : 0.036 0.199 3870 Planarity : 0.004 0.051 3150 Dihedral : 22.455 153.895 6570 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.24 % Allowed : 17.26 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.63 (0.17), residues: 2460 helix: 3.02 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 3.07 (0.70), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 3 46 PHE 0.011 0.002 PHE J 69 TRP 0.013 0.001 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (23040) covalent geometry : angle 0.49742 / 0.26 (30990) hydrogen bonds : bond 0.06147 / 4.20 ( 1980) hydrogen bonds : angle 3.47938 / 2.61 ( 5940) Misc. bond : bond 0.00170 / 0.12 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 307 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8966 (ttt-90) cc_final: 0.8520 (mtp85) REVERT: A 54 ASP cc_start: 0.8596 (m-30) cc_final: 0.8278 (m-30) REVERT: A 81 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8701 (tm-30) REVERT: C 81 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 11 ASP cc_start: 0.8726 (m-30) cc_final: 0.8264 (m-30) REVERT: D 53 GLU cc_start: 0.8417 (tt0) cc_final: 0.7846 (tt0) REVERT: E 81 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8742 (tm-30) REVERT: F 53 GLU cc_start: 0.8458 (tt0) cc_final: 0.8066 (tt0) REVERT: G 53 GLU cc_start: 0.8091 (tt0) cc_final: 0.7751 (tt0) REVERT: H 81 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8582 (tm-30) REVERT: I 53 GLU cc_start: 0.8377 (tt0) cc_final: 0.7889 (tt0) REVERT: I 81 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8643 (tm-30) REVERT: J 53 GLU cc_start: 0.8447 (tt0) cc_final: 0.8127 (tt0) REVERT: J 81 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8739 (tm-30) REVERT: K 53 GLU cc_start: 0.8521 (tt0) cc_final: 0.8036 (tt0) REVERT: K 81 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8655 (tm-30) REVERT: M 46 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8337 (mtm110) REVERT: M 53 GLU cc_start: 0.8576 (tt0) cc_final: 0.8146 (tt0) REVERT: N 81 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8755 (tm-30) REVERT: P 53 GLU cc_start: 0.8481 (tt0) cc_final: 0.7993 (tt0) REVERT: P 81 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8586 (tm-30) REVERT: Q 53 GLU cc_start: 0.8320 (tt0) cc_final: 0.7895 (tt0) REVERT: T 35 ARG cc_start: 0.9078 (ttt90) cc_final: 0.8777 (mmm160) REVERT: T 53 GLU cc_start: 0.8302 (tt0) cc_final: 0.7851 (tt0) REVERT: T 81 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8804 (tm-30) REVERT: U 53 GLU cc_start: 0.8294 (tt0) cc_final: 0.7976 (tt0) REVERT: U 81 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8768 (tm-30) REVERT: V 53 GLU cc_start: 0.8355 (tt0) cc_final: 0.7966 (tt0) REVERT: V 81 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8603 (tm-30) REVERT: W 53 GLU cc_start: 0.8360 (tt0) cc_final: 0.7795 (tt0) REVERT: X 81 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8628 (tm-30) REVERT: Y 53 GLU cc_start: 0.8329 (tt0) cc_final: 0.7863 (tt0) REVERT: 0 53 GLU cc_start: 0.8366 (tt0) cc_final: 0.8003 (tt0) REVERT: 0 74 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.7974 (ttp80) REVERT: 0 81 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8742 (tm-30) REVERT: 1 53 GLU cc_start: 0.8327 (tt0) cc_final: 0.7830 (tt0) REVERT: 1 74 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.7911 (ttp80) REVERT: 1 81 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8667 (tm-30) REVERT: 2 53 GLU cc_start: 0.8403 (tt0) cc_final: 0.7795 (tt0) REVERT: 2 74 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.7925 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8729 (tm-30) REVERT: 3 81 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8756 (tm-30) outliers start: 25 outliers final: 19 residues processed: 323 average time/residue: 0.1442 time to fit residues: 73.2561 Evaluate side-chains 325 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086367 restraints weight = 35205.796| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.58 r_work: 0.2866 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23121 Z= 0.170 Angle : 0.520 5.466 30990 Z= 0.276 Chirality : 0.037 0.208 3870 Planarity : 0.005 0.063 3150 Dihedral : 22.658 154.277 6570 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.34 % Allowed : 17.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.57 (0.17), residues: 2460 helix: 2.99 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.99 (0.70), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 3 46 PHE 0.012 0.002 PHE B 69 TRP 0.014 0.001 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (23040) covalent geometry : angle 0.51997 / 0.28 (30990) hydrogen bonds : bond 0.06567 / 4.49 ( 1980) hydrogen bonds : angle 3.58123 / 2.69 ( 5940) Misc. bond : bond 0.00165 / 0.12 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 316 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8921 (tm-30) REVERT: A 54 ASP cc_start: 0.8607 (m-30) cc_final: 0.8297 (m-30) REVERT: A 81 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8717 (tm-30) REVERT: C 81 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8517 (tm-30) REVERT: D 11 ASP cc_start: 0.8747 (m-30) cc_final: 0.8332 (m-30) REVERT: D 53 GLU cc_start: 0.8463 (tt0) cc_final: 0.7876 (tt0) REVERT: E 81 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8749 (tm-30) REVERT: F 53 GLU cc_start: 0.8495 (tt0) cc_final: 0.8060 (tt0) REVERT: G 53 GLU cc_start: 0.8108 (tt0) cc_final: 0.7793 (tt0) REVERT: H 81 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8592 (tm-30) REVERT: I 53 GLU cc_start: 0.8433 (tt0) cc_final: 0.7918 (tt0) REVERT: I 81 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8635 (tm-30) REVERT: J 53 GLU cc_start: 0.8478 (tt0) cc_final: 0.8160 (tt0) REVERT: K 53 GLU cc_start: 0.8532 (tt0) cc_final: 0.8028 (tt0) REVERT: K 81 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8662 (tm-30) REVERT: L 53 GLU cc_start: 0.8539 (tt0) cc_final: 0.7990 (tt0) REVERT: M 46 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8340 (mtm110) REVERT: M 53 GLU cc_start: 0.8644 (tt0) cc_final: 0.8305 (tt0) REVERT: N 46 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.8188 (mtm110) REVERT: N 81 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8757 (tm-30) REVERT: P 81 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8558 (tm-30) REVERT: Q 53 GLU cc_start: 0.8469 (tt0) cc_final: 0.7941 (tt0) REVERT: S 53 GLU cc_start: 0.8462 (tt0) cc_final: 0.8063 (tt0) REVERT: T 35 ARG cc_start: 0.9077 (ttt90) cc_final: 0.8840 (mmm160) REVERT: T 53 GLU cc_start: 0.8343 (tt0) cc_final: 0.7868 (tt0) REVERT: T 81 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8815 (tm-30) REVERT: U 53 GLU cc_start: 0.8304 (tt0) cc_final: 0.7995 (tt0) REVERT: U 81 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8751 (tm-30) REVERT: V 53 GLU cc_start: 0.8387 (tt0) cc_final: 0.7954 (tt0) REVERT: V 81 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8605 (tm-30) REVERT: W 53 GLU cc_start: 0.8389 (tt0) cc_final: 0.7823 (tt0) REVERT: Y 53 GLU cc_start: 0.8388 (tt0) cc_final: 0.7910 (tt0) REVERT: 0 53 GLU cc_start: 0.8401 (tt0) cc_final: 0.8032 (tt0) REVERT: 0 74 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.7958 (ttp80) REVERT: 0 81 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8751 (tm-30) REVERT: 1 53 GLU cc_start: 0.8292 (tt0) cc_final: 0.7779 (tt0) REVERT: 1 74 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.7869 (ttp80) REVERT: 1 81 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8699 (tm-30) REVERT: 2 53 GLU cc_start: 0.8428 (tt0) cc_final: 0.7818 (tt0) REVERT: 2 74 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.7880 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8670 (tm-30) REVERT: 3 81 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8763 (tm-30) outliers start: 27 outliers final: 20 residues processed: 331 average time/residue: 0.1603 time to fit residues: 80.9007 Evaluate side-chains 336 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 127 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090131 restraints weight = 35111.247| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.55 r_work: 0.2932 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23121 Z= 0.144 Angle : 0.496 5.603 30990 Z= 0.266 Chirality : 0.035 0.195 3870 Planarity : 0.005 0.067 3150 Dihedral : 21.895 157.377 6570 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.04 % Allowed : 17.86 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.66 (0.17), residues: 2460 helix: 3.05 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 3.01 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 46 PHE 0.007 0.001 PHE D 69 TRP 0.012 0.001 TRP 3 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (23040) covalent geometry : angle 0.49647 / 0.27 (30990) hydrogen bonds : bond 0.05858 / 4.01 ( 1980) hydrogen bonds : angle 3.42769 / 2.58 ( 5940) Misc. bond : bond 0.00152 / 0.11 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8608 (m-30) cc_final: 0.8290 (m-30) REVERT: A 81 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8714 (tm-30) REVERT: C 81 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 11 ASP cc_start: 0.8710 (m-30) cc_final: 0.8248 (m-30) REVERT: D 53 GLU cc_start: 0.8414 (tt0) cc_final: 0.7843 (tt0) REVERT: E 81 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8748 (tm-30) REVERT: F 53 GLU cc_start: 0.8485 (tt0) cc_final: 0.8074 (tt0) REVERT: G 53 GLU cc_start: 0.8068 (tt0) cc_final: 0.7719 (tt0) REVERT: H 81 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8584 (tm-30) REVERT: I 53 GLU cc_start: 0.8416 (tt0) cc_final: 0.7861 (tt0) REVERT: I 81 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8631 (tm-30) REVERT: J 53 GLU cc_start: 0.8442 (tt0) cc_final: 0.8132 (tt0) REVERT: J 81 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8681 (tm-30) REVERT: K 53 GLU cc_start: 0.8516 (tt0) cc_final: 0.8043 (tt0) REVERT: K 81 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8650 (tm-30) REVERT: M 53 GLU cc_start: 0.8575 (tt0) cc_final: 0.8149 (tt0) REVERT: N 81 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8769 (tm-30) REVERT: P 81 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8545 (tm-30) REVERT: Q 53 GLU cc_start: 0.8310 (tt0) cc_final: 0.7869 (tt0) REVERT: T 35 ARG cc_start: 0.9080 (ttt90) cc_final: 0.8770 (mmm160) REVERT: T 53 GLU cc_start: 0.8301 (tt0) cc_final: 0.7832 (tt0) REVERT: T 81 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8844 (tm-30) REVERT: U 53 GLU cc_start: 0.8245 (tt0) cc_final: 0.7942 (tt0) REVERT: U 81 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8762 (tm-30) REVERT: V 53 GLU cc_start: 0.8349 (tt0) cc_final: 0.7943 (tt0) REVERT: V 81 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8611 (tm-30) REVERT: W 53 GLU cc_start: 0.8356 (tt0) cc_final: 0.7780 (tt0) REVERT: W 81 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8792 (tm-30) REVERT: X 81 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8651 (tm-30) REVERT: Y 53 GLU cc_start: 0.8326 (tt0) cc_final: 0.7861 (tt0) REVERT: 0 53 GLU cc_start: 0.8367 (tt0) cc_final: 0.8012 (tt0) REVERT: 0 74 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.7990 (ttp80) REVERT: 0 81 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8751 (tm-30) REVERT: 1 53 GLU cc_start: 0.8329 (tt0) cc_final: 0.7776 (tt0) REVERT: 1 74 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.7929 (ttp80) REVERT: 1 81 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8663 (tm-30) REVERT: 2 53 GLU cc_start: 0.8378 (tt0) cc_final: 0.7765 (tt0) REVERT: 2 74 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.7944 (ttp-170) REVERT: 2 81 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8753 (tm-30) REVERT: 3 81 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8748 (tm-30) outliers start: 21 outliers final: 20 residues processed: 317 average time/residue: 0.1389 time to fit residues: 70.8644 Evaluate side-chains 327 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087629 restraints weight = 35079.584| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.59 r_work: 0.2890 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23121 Z= 0.161 Angle : 0.520 5.665 30990 Z= 0.275 Chirality : 0.036 0.197 3870 Planarity : 0.005 0.060 3150 Dihedral : 22.051 153.785 6570 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.24 % Allowed : 17.81 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.17), residues: 2460 helix: 3.02 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 3.05 (0.70), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 3 46 PHE 0.011 0.002 PHE C 69 TRP 0.014 0.001 TRP 3 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (23040) covalent geometry : angle 0.51951 / 0.28 (30990) hydrogen bonds : bond 0.06289 / 4.30 ( 1980) hydrogen bonds : angle 3.52115 / 2.65 ( 5940) Misc. bond : bond 0.00158 / 0.12 ( 81) =============================================================================== Job complete usr+sys time: 3301.73 seconds wall clock time: 57 minutes 31.21 seconds (3451.21 seconds total)