Starting phenix.real_space_refine on Mon Jul 6 14:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuy_60915/07_2026/9iuy_60915.map" } resolution = 1.51 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.101 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: 7 Type Number sf(0) Gaussians K 24 8.98 5 Fe 6 7.16 5 Mg 32 5.21 5 S 192 5.16 5 C 21432 2.51 5 N 6024 2.21 5 O 9840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s 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: 37550 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "B" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "D" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "E" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "F" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "G" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "H" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "I" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "J" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "K" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "L" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "M" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "N" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "O" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "P" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "Q" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "R" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "S" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "T" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "U" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "V" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "W" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 1, ' FE': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "E" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "F" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "G" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "H" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "I" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "J" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "L" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "N" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "O" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "Q" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "R" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "S" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "T" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "U" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "V" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "W" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "X" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Time building chain proxies: 7.64, per 1000 atoms: 0.20 Number of scatterers: 37550 At special positions: 0 Unit cell: (132.84, 132.84, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 K 24 19.00 S 192 16.00 Mg 32 11.99 O 9840 8.00 N 6024 7.00 C 21432 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=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 6.65 Time building geometry restraints manager: 4.22 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: 11640 1.34 - 1.46: 6383 1.46 - 1.58: 16585 1.58 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34920 Sorted by residual: bond pdb=" N ASP T 89 " pdb=" CA ASP T 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP D 89 " pdb=" CA ASP D 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP F 89 " pdb=" CA ASP F 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP A 89 " pdb=" CA ASP A 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP C 89 " pdb=" CA ASP C 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 44398 1.23 - 2.47: 2042 2.47 - 3.70: 456 3.70 - 4.94: 48 4.94 - 6.17: 48 Bond angle restraints: 46992 Sorted by residual: angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP G 93 " pdb=" N GLU G 94 " pdb=" CA GLU G 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 46987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 19200 15.13 - 30.25: 1512 30.25 - 45.38: 216 45.38 - 60.51: 216 60.51 - 75.63: 72 Dihedral angle restraints: 21216 sinusoidal: 8832 harmonic: 12384 Sorted by residual: dihedral pdb=" CA TRP D 93 " pdb=" C TRP D 93 " pdb=" N GLU D 94 " pdb=" CA GLU D 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP U 93 " pdb=" C TRP U 93 " pdb=" N GLU U 94 " pdb=" CA GLU U 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP H 93 " pdb=" C TRP H 93 " pdb=" N GLU H 94 " pdb=" CA GLU H 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 21213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3719 0.038 - 0.076: 817 0.076 - 0.114: 240 0.114 - 0.152: 96 0.152 - 0.190: 24 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CG LEU J 72 " pdb=" CB LEU J 72 " pdb=" CD1 LEU J 72 " pdb=" CD2 LEU J 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU C 72 " pdb=" CB LEU C 72 " pdb=" CD1 LEU C 72 " pdb=" CD2 LEU C 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU X 72 " pdb=" CB LEU X 72 " pdb=" CD1 LEU X 72 " pdb=" CD2 LEU X 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 4893 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " -0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR Q 32 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 32 " 0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR G 32 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR G 32 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR G 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR G 32 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 32 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " 0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR F 32 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 2736 2.69 - 3.30: 47113 3.30 - 3.92: 93227 3.92 - 4.53: 127654 4.53 - 5.14: 177578 Nonbonded interactions: 448308 Sorted by model distance: nonbonded pdb="MG MG U 201 " pdb=" O HOH U 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG L 201 " pdb=" O HOH L 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 201 " pdb=" O HOH D 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG M 201 " pdb=" O HOH M 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG E 201 " pdb=" O HOH E 336 " model vdw 2.080 2.170 ... (remaining 448303 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 202) selection = (chain 'B' and resid 4 through 202) selection = (chain 'C' and resid 4 through 202) selection = (chain 'D' and resid 4 through 202) selection = (chain 'E' and resid 4 through 202) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 4 through 202) selection = (chain 'I' and resid 4 through 202) selection = (chain 'J' and resid 4 through 202) selection = chain 'K' selection = (chain 'L' and resid 4 through 202) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 4 through 202) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 4.900 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.910 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.004 0.033 34920 Z= 0.216 Angle : 0.649 6.173 46992 Z= 0.376 Chirality : 0.041 0.190 4896 Planarity : 0.005 0.034 6192 Dihedral : 13.662 75.634 13200 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.29 (0.13), residues: 4128 helix: 3.41 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 76 TYR 0.054 0.004 TYR W 32 PHE 0.019 0.004 PHE W 41 TRP 0.012 0.004 TRP K 93 HIS 0.006 0.002 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (34920) covalent geometry : angle 0.64940 / 0.38 (46992) hydrogen bonds : bond 0.07430 / 4.92 ( 2640) hydrogen bonds : angle 4.17721 / 3.08 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 1.539 Fit side-chains outliers start: 0 outliers final: 24 residues processed: 1032 average time/residue: 0.9430 time to fit residues: 1115.5006 Evaluate side-chains 960 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 936 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.177701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.165010 restraints weight = 12615.665| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 0.27 r_work: 0.3712 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 0.92 restraints_weight: 0.2500 r_work: 0.3264 rms_B_bonded: 2.54 restraints_weight: 0.1250 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34920 Z= 0.198 Angle : 0.642 6.335 46992 Z= 0.348 Chirality : 0.038 0.125 4896 Planarity : 0.004 0.021 6192 Dihedral : 4.748 21.440 4656 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.24 (0.13), residues: 4128 helix: 3.38 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.54 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 63 TYR 0.023 0.003 TYR D 32 PHE 0.018 0.003 PHE A 41 TRP 0.014 0.004 TRP X 93 HIS 0.006 0.002 HIS R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (34920) covalent geometry : angle 0.64151 / 0.35 (46992) hydrogen bonds : bond 0.05688 / 3.80 ( 2640) hydrogen bonds : angle 3.90600 / 2.88 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 959 time to evaluate : 1.116 Fit side-chains REVERT: A 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7261 (mtp85) REVERT: B 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7263 (mtp85) REVERT: C 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7264 (mtp85) REVERT: D 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7260 (mtp85) REVERT: E 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7259 (mtp85) REVERT: F 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7262 (mtp85) REVERT: G 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7265 (mtp85) REVERT: H 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7265 (mtp85) REVERT: I 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7266 (mtp85) REVERT: J 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7265 (mtp85) REVERT: K 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7266 (mtp85) REVERT: L 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7264 (mtp85) REVERT: M 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7266 (mtp85) REVERT: N 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7266 (mtp85) REVERT: O 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7265 (mtp85) REVERT: P 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7265 (mtp85) REVERT: Q 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7263 (mtp85) REVERT: R 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7265 (mtp85) REVERT: S 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7266 (mtp85) REVERT: T 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7261 (mtp85) REVERT: U 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7260 (mtp85) REVERT: V 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7264 (mtp85) REVERT: W 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7263 (mtp85) REVERT: X 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7263 (mtp85) outliers start: 0 outliers final: 0 residues processed: 959 average time/residue: 1.0030 time to fit residues: 1095.2691 Evaluate side-chains 936 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 936 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 17 optimal weight: 20.0000 chunk 293 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 141 GLN B 25 ASN B 141 GLN C 25 ASN D 25 ASN E 25 ASN F 25 ASN F 141 GLN G 25 ASN G 141 GLN H 25 ASN I 25 ASN I 141 GLN J 25 ASN K 25 ASN K 141 GLN L 25 ASN L 141 GLN M 25 ASN M 141 GLN N 25 ASN N 141 GLN O 25 ASN P 25 ASN P 141 GLN Q 25 ASN Q 141 GLN R 25 ASN S 25 ASN S 141 GLN T 25 ASN T 141 GLN U 25 ASN V 25 ASN V 141 GLN W 25 ASN W 141 GLN X 25 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167246 restraints weight = 12696.554| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.27 r_work: 0.3743 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 0.91 restraints_weight: 0.2500 r_work: 0.3302 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34920 Z= 0.136 Angle : 0.537 5.484 46992 Z= 0.289 Chirality : 0.036 0.122 4896 Planarity : 0.003 0.021 6192 Dihedral : 4.349 21.503 4560 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.81 % Allowed : 5.03 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.59 (0.13), residues: 4128 helix: 3.61 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.76 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 63 TYR 0.015 0.002 TYR E 137 PHE 0.014 0.002 PHE R 41 TRP 0.012 0.003 TRP I 93 HIS 0.004 0.001 HIS H 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (34920) covalent geometry : angle 0.53710 / 0.29 (46992) hydrogen bonds : bond 0.04901 / 3.28 ( 2640) hydrogen bonds : angle 3.66336 / 2.70 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 939 time to evaluate : 1.193 Fit side-chains REVERT: A 90 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7254 (mtp85) REVERT: A 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8042 (mmtm) REVERT: B 90 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7252 (mtp85) REVERT: B 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8039 (mmtm) REVERT: C 90 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7257 (mtp85) REVERT: C 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8040 (mmtm) REVERT: D 90 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7254 (mtp85) REVERT: D 157 LYS cc_start: 0.8290 (mttp) cc_final: 0.8036 (mmtm) REVERT: E 90 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7242 (mtp85) REVERT: E 157 LYS cc_start: 0.8290 (mttp) cc_final: 0.8035 (mmtm) REVERT: F 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7246 (mtp85) REVERT: F 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8040 (mmtm) REVERT: G 90 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7265 (mtp85) REVERT: G 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8042 (mmtm) REVERT: H 90 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7266 (mtp85) REVERT: H 157 LYS cc_start: 0.8295 (mttp) cc_final: 0.8039 (mmtm) REVERT: I 90 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7266 (mtp85) REVERT: I 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8038 (mmtm) REVERT: J 90 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7260 (mtp85) REVERT: J 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8039 (mmtm) REVERT: K 90 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7253 (mtp85) REVERT: K 157 LYS cc_start: 0.8297 (mttp) cc_final: 0.8041 (mmtm) REVERT: L 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7244 (mtp85) REVERT: L 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8042 (mmtm) REVERT: M 90 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7260 (mtp85) REVERT: M 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8038 (mmtm) REVERT: N 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7245 (mtp85) REVERT: N 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8039 (mmtm) REVERT: O 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7250 (mtp85) REVERT: O 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8039 (mmtm) REVERT: P 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7241 (mtp85) REVERT: P 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8044 (mmtm) REVERT: Q 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7251 (mtp85) REVERT: Q 157 LYS cc_start: 0.8298 (mttp) cc_final: 0.8041 (mmtm) REVERT: R 90 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7259 (mtp85) REVERT: R 157 LYS cc_start: 0.8295 (mttp) cc_final: 0.8040 (mmtm) REVERT: S 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7250 (mtp85) REVERT: S 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8041 (mmtm) REVERT: T 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7252 (mtp85) REVERT: T 157 LYS cc_start: 0.8298 (mttp) cc_final: 0.8041 (mmtm) REVERT: U 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7249 (mtp85) REVERT: U 157 LYS cc_start: 0.8292 (mttp) cc_final: 0.8036 (mmtm) REVERT: V 63 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7983 (ttt90) REVERT: V 90 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7252 (mtp85) REVERT: V 157 LYS cc_start: 0.8297 (mttp) cc_final: 0.8041 (mmtm) REVERT: W 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7244 (mtp85) REVERT: W 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8046 (mmtm) REVERT: X 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7252 (mtp85) REVERT: X 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8039 (mmtm) outliers start: 30 outliers final: 9 residues processed: 939 average time/residue: 1.0131 time to fit residues: 1081.6808 Evaluate side-chains 907 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 898 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.180106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.167709 restraints weight = 12672.288| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 0.26 r_work: 0.3751 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3309 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34920 Z= 0.130 Angle : 0.531 5.209 46992 Z= 0.286 Chirality : 0.036 0.119 4896 Planarity : 0.003 0.023 6192 Dihedral : 4.374 23.334 4560 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.84 % Allowed : 5.30 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.74 (0.13), residues: 4128 helix: 3.76 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.75 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.014 0.001 TYR Q 137 PHE 0.015 0.002 PHE C 41 TRP 0.013 0.003 TRP X 93 HIS 0.004 0.001 HIS W 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (34920) covalent geometry : angle 0.53088 / 0.29 (46992) hydrogen bonds : bond 0.04815 / 3.23 ( 2640) hydrogen bonds : angle 3.64446 / 2.68 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 847 time to evaluate : 1.215 Fit side-chains REVERT: A 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7239 (mtp85) REVERT: A 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8044 (mmtm) REVERT: B 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7233 (mtp85) REVERT: B 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8045 (mmtm) REVERT: C 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7231 (mtp85) REVERT: C 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8047 (mmtm) REVERT: D 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7237 (mtp85) REVERT: D 157 LYS cc_start: 0.8299 (mttp) cc_final: 0.8049 (mmtm) REVERT: E 90 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7225 (mtp85) REVERT: E 157 LYS cc_start: 0.8295 (mttp) cc_final: 0.8041 (mmtm) REVERT: F 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7230 (mtp85) REVERT: F 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8041 (mmtm) REVERT: G 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7242 (mtp85) REVERT: G 157 LYS cc_start: 0.8290 (mttp) cc_final: 0.8032 (mmtm) REVERT: H 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7244 (mtp85) REVERT: H 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8051 (mmtm) REVERT: I 90 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7246 (mtp85) REVERT: I 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8050 (mmtm) REVERT: J 90 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7250 (mtp85) REVERT: J 157 LYS cc_start: 0.8306 (mttp) cc_final: 0.8054 (mmtm) REVERT: K 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7234 (mtp85) REVERT: K 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8053 (mmtm) REVERT: L 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7239 (mtp85) REVERT: L 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8046 (mmtm) REVERT: M 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7239 (mtp85) REVERT: M 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8046 (mmtm) REVERT: N 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7233 (mtp85) REVERT: N 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8049 (mmtm) REVERT: O 90 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7227 (mtp85) REVERT: O 157 LYS cc_start: 0.8297 (mttp) cc_final: 0.8045 (mmtm) REVERT: P 90 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7229 (mtp85) REVERT: P 157 LYS cc_start: 0.8294 (mttp) cc_final: 0.8044 (mmtm) REVERT: Q 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7241 (mtp85) REVERT: Q 157 LYS cc_start: 0.8295 (mttp) cc_final: 0.8040 (mmtm) REVERT: R 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: R 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8044 (mmtm) REVERT: S 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7236 (mtp85) REVERT: S 157 LYS cc_start: 0.8291 (mttp) cc_final: 0.8040 (mmtm) REVERT: T 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7236 (mtp85) REVERT: T 157 LYS cc_start: 0.8296 (mttp) cc_final: 0.8041 (mmtm) REVERT: U 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7231 (mtp85) REVERT: U 157 LYS cc_start: 0.8299 (mttp) cc_final: 0.8043 (mmtm) REVERT: V 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7232 (mtp85) REVERT: V 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8048 (mmtm) REVERT: W 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7243 (mtp85) REVERT: W 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8050 (mmtm) REVERT: X 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7239 (mtp85) REVERT: X 157 LYS cc_start: 0.8293 (mttp) cc_final: 0.8041 (mmtm) outliers start: 68 outliers final: 24 residues processed: 895 average time/residue: 1.0081 time to fit residues: 1026.3594 Evaluate side-chains 875 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 851 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 213 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.175876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163325 restraints weight = 12528.037| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 0.27 r_work: 0.3698 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34920 Z= 0.246 Angle : 0.713 5.612 46992 Z= 0.388 Chirality : 0.041 0.167 4896 Planarity : 0.004 0.034 6192 Dihedral : 4.586 22.019 4560 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.00 % Allowed : 5.95 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.22 (0.13), residues: 4128 helix: 3.33 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 63 TYR 0.018 0.003 TYR K 137 PHE 0.021 0.004 PHE I 41 TRP 0.012 0.004 TRP K 93 HIS 0.007 0.002 HIS J 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (34920) covalent geometry : angle 0.71277 / 0.39 (46992) hydrogen bonds : bond 0.06010 / 4.02 ( 2640) hydrogen bonds : angle 3.98660 / 2.93 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 886 time to evaluate : 1.384 Fit side-chains outliers start: 37 outliers final: 24 residues processed: 910 average time/residue: 0.9876 time to fit residues: 1021.0455 Evaluate side-chains 960 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 936 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 276 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.176765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.164164 restraints weight = 12549.814| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.27 r_work: 0.3708 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3266 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34920 Z= 0.211 Angle : 0.659 5.640 46992 Z= 0.359 Chirality : 0.039 0.141 4896 Planarity : 0.004 0.043 6192 Dihedral : 4.595 22.595 4560 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.27 % Allowed : 6.82 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.28 (0.13), residues: 4128 helix: 3.35 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 90 TYR 0.016 0.003 TYR I 137 PHE 0.020 0.003 PHE R 41 TRP 0.014 0.004 TRP P 93 HIS 0.006 0.002 HIS J 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (34920) covalent geometry : angle 0.65939 / 0.36 (46992) hydrogen bonds : bond 0.05731 / 3.83 ( 2640) hydrogen bonds : angle 3.91756 / 2.88 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 936 time to evaluate : 1.211 Fit side-chains REVERT: K 165 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8101 (tpp) REVERT: N 165 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8106 (tpp) REVERT: O 165 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (tpp) REVERT: R 165 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (tpp) REVERT: T 165 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8107 (tpp) REVERT: U 165 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8102 (tpp) REVERT: W 165 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8104 (tpp) REVERT: X 165 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8104 (tpp) outliers start: 47 outliers final: 24 residues processed: 936 average time/residue: 1.0360 time to fit residues: 1101.8690 Evaluate side-chains 940 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 908 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 13 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 302 optimal weight: 0.6980 chunk 299 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.179009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166526 restraints weight = 12639.625| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 0.26 r_work: 0.3734 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.3295 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34920 Z= 0.148 Angle : 0.568 5.602 46992 Z= 0.307 Chirality : 0.036 0.118 4896 Planarity : 0.003 0.023 6192 Dihedral : 4.475 23.170 4560 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.87 % Allowed : 7.12 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.61 (0.13), residues: 4128 helix: 3.59 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 90 TYR 0.013 0.002 TYR D 137 PHE 0.016 0.003 PHE A 41 TRP 0.014 0.003 TRP P 93 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (34920) covalent geometry : angle 0.56759 / 0.31 (46992) hydrogen bonds : bond 0.05088 / 3.41 ( 2640) hydrogen bonds : angle 3.73458 / 2.75 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 903 time to evaluate : 1.029 Fit side-chains REVERT: A 157 LYS cc_start: 0.8287 (mttp) cc_final: 0.8032 (mmtm) REVERT: B 157 LYS cc_start: 0.8277 (mttp) cc_final: 0.8026 (mmtm) REVERT: C 157 LYS cc_start: 0.8279 (mttp) cc_final: 0.8029 (mmtm) REVERT: D 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8024 (mmtm) REVERT: E 157 LYS cc_start: 0.8293 (mttp) cc_final: 0.8037 (mmtm) REVERT: F 157 LYS cc_start: 0.8292 (mttp) cc_final: 0.8035 (mmtm) REVERT: G 157 LYS cc_start: 0.8282 (mttp) cc_final: 0.8034 (mmtm) REVERT: G 165 MET cc_start: 0.8281 (tpp) cc_final: 0.8049 (tpp) REVERT: H 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8027 (mmtm) REVERT: I 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8026 (mmtm) REVERT: J 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8025 (mmtm) REVERT: K 157 LYS cc_start: 0.8268 (mttp) cc_final: 0.8020 (mmtm) REVERT: L 157 LYS cc_start: 0.8284 (mttp) cc_final: 0.8029 (mmtm) REVERT: M 157 LYS cc_start: 0.8273 (mttp) cc_final: 0.8022 (mmtm) REVERT: N 157 LYS cc_start: 0.8271 (mttp) cc_final: 0.8023 (mmtm) REVERT: O 157 LYS cc_start: 0.8273 (mttp) cc_final: 0.8022 (mmtm) REVERT: P 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8024 (mmtm) REVERT: Q 157 LYS cc_start: 0.8277 (mttp) cc_final: 0.8025 (mmtm) REVERT: R 157 LYS cc_start: 0.8281 (mttp) cc_final: 0.8029 (mmtm) REVERT: S 157 LYS cc_start: 0.8278 (mttp) cc_final: 0.8026 (mmtm) REVERT: T 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8022 (mmtm) REVERT: U 157 LYS cc_start: 0.8272 (mttp) cc_final: 0.8021 (mmtm) REVERT: V 63 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7957 (ttt90) REVERT: V 157 LYS cc_start: 0.8273 (mttp) cc_final: 0.8021 (mmtm) REVERT: V 165 MET cc_start: 0.8300 (tpp) cc_final: 0.8071 (tpp) REVERT: W 157 LYS cc_start: 0.8278 (mttp) cc_final: 0.8029 (mmtm) REVERT: X 157 LYS cc_start: 0.8274 (mttp) cc_final: 0.8023 (mmtm) outliers start: 32 outliers final: 24 residues processed: 914 average time/residue: 1.0010 time to fit residues: 1041.9970 Evaluate side-chains 954 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 930 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 238 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 365 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163393 restraints weight = 12498.807| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.26 r_work: 0.3702 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3258 rms_B_bonded: 2.46 restraints_weight: 0.1250 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34920 Z= 0.257 Angle : 0.719 6.105 46992 Z= 0.395 Chirality : 0.041 0.167 4896 Planarity : 0.004 0.025 6192 Dihedral : 4.596 21.953 4560 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 6.57 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.19 (0.13), residues: 4128 helix: 3.34 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.67 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 156 TYR 0.018 0.003 TYR V 137 PHE 0.022 0.004 PHE N 41 TRP 0.012 0.005 TRP F 93 HIS 0.007 0.002 HIS L 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (34920) covalent geometry : angle 0.71885 / 0.39 (46992) hydrogen bonds : bond 0.06107 / 4.08 ( 2640) hydrogen bonds : angle 4.01380 / 2.95 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 936 time to evaluate : 1.315 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 936 average time/residue: 1.0533 time to fit residues: 1117.3251 Evaluate side-chains 960 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 936 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 315 optimal weight: 3.9990 chunk 323 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 368 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.167328 restraints weight = 12654.525| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.26 r_work: 0.3736 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 0.88 restraints_weight: 0.2500 r_work: 0.3295 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34920 Z= 0.155 Angle : 0.581 5.797 46992 Z= 0.315 Chirality : 0.037 0.118 4896 Planarity : 0.003 0.021 6192 Dihedral : 4.501 23.053 4560 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.53 (0.13), residues: 4128 helix: 3.59 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.74 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 156 TYR 0.013 0.002 TYR V 137 PHE 0.016 0.003 PHE P 41 TRP 0.014 0.004 TRP W 93 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (34920) covalent geometry : angle 0.58105 / 0.31 (46992) hydrogen bonds : bond 0.05177 / 3.47 ( 2640) hydrogen bonds : angle 3.76483 / 2.77 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 913 time to evaluate : 1.176 Fit side-chains REVERT: A 157 LYS cc_start: 0.8286 (mttp) cc_final: 0.8030 (mmtm) REVERT: A 165 MET cc_start: 0.8325 (tpp) cc_final: 0.8122 (tpp) REVERT: B 157 LYS cc_start: 0.8289 (mttp) cc_final: 0.8014 (mmtm) REVERT: C 157 LYS cc_start: 0.8284 (mttp) cc_final: 0.8013 (mmtm) REVERT: C 165 MET cc_start: 0.8320 (tpp) cc_final: 0.8116 (tpp) REVERT: D 157 LYS cc_start: 0.8285 (mttp) cc_final: 0.8013 (mmtm) REVERT: D 165 MET cc_start: 0.8327 (tpp) cc_final: 0.8124 (tpp) REVERT: E 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8002 (mmtm) REVERT: E 165 MET cc_start: 0.8322 (tpp) cc_final: 0.8118 (tpp) REVERT: F 157 LYS cc_start: 0.8291 (mttp) cc_final: 0.8034 (mmtm) REVERT: F 165 MET cc_start: 0.8324 (tpp) cc_final: 0.8118 (tpp) REVERT: G 157 LYS cc_start: 0.8280 (mttp) cc_final: 0.8027 (mmtm) REVERT: G 165 MET cc_start: 0.8332 (tpp) cc_final: 0.8088 (tpp) REVERT: H 157 LYS cc_start: 0.8285 (mttp) cc_final: 0.8014 (mmtm) REVERT: H 165 MET cc_start: 0.8324 (tpp) cc_final: 0.8097 (tpp) REVERT: I 157 LYS cc_start: 0.8284 (mttp) cc_final: 0.8012 (mmtm) REVERT: I 165 MET cc_start: 0.8336 (tpp) cc_final: 0.8135 (tpp) REVERT: J 157 LYS cc_start: 0.8287 (mttp) cc_final: 0.8014 (mmtm) REVERT: J 165 MET cc_start: 0.8336 (tpp) cc_final: 0.8133 (tpp) REVERT: K 157 LYS cc_start: 0.8282 (mttp) cc_final: 0.8012 (mmtm) REVERT: L 157 LYS cc_start: 0.8289 (mttp) cc_final: 0.8012 (mmtm) REVERT: L 165 MET cc_start: 0.8328 (tpp) cc_final: 0.8122 (tpp) REVERT: M 157 LYS cc_start: 0.8288 (mttp) cc_final: 0.8013 (mmtm) REVERT: M 165 MET cc_start: 0.8338 (tpp) cc_final: 0.8135 (tpp) REVERT: N 157 LYS cc_start: 0.8285 (mttp) cc_final: 0.8014 (mmtm) REVERT: O 157 LYS cc_start: 0.8290 (mttp) cc_final: 0.8016 (mmtm) REVERT: P 157 LYS cc_start: 0.8286 (mttp) cc_final: 0.8011 (mmtm) REVERT: P 165 MET cc_start: 0.8325 (tpp) cc_final: 0.8121 (tpp) REVERT: Q 157 LYS cc_start: 0.8281 (mttp) cc_final: 0.8008 (mmtm) REVERT: Q 165 MET cc_start: 0.8337 (tpp) cc_final: 0.8132 (tpp) REVERT: R 157 LYS cc_start: 0.8289 (mttp) cc_final: 0.8019 (mmtm) REVERT: S 157 LYS cc_start: 0.8287 (mttp) cc_final: 0.8013 (mmtm) REVERT: T 157 LYS cc_start: 0.8281 (mttp) cc_final: 0.8010 (mmtm) REVERT: T 165 MET cc_start: 0.8288 (tpp) cc_final: 0.8041 (tpp) REVERT: U 157 LYS cc_start: 0.8282 (mttp) cc_final: 0.8008 (mmtm) REVERT: V 63 ARG cc_start: 0.8187 (ttp-170) cc_final: 0.7974 (ttt90) REVERT: V 157 LYS cc_start: 0.8286 (mttp) cc_final: 0.8014 (mmtm) REVERT: V 165 MET cc_start: 0.8327 (tpp) cc_final: 0.8113 (tpp) REVERT: W 157 LYS cc_start: 0.8286 (mttp) cc_final: 0.8014 (mmtm) REVERT: X 157 LYS cc_start: 0.8283 (mttp) cc_final: 0.8012 (mmtm) outliers start: 24 outliers final: 24 residues processed: 930 average time/residue: 0.9949 time to fit residues: 1053.4177 Evaluate side-chains 917 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 893 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 377 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 398 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.177184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.164805 restraints weight = 12542.745| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 0.26 r_work: 0.3707 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3262 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34920 Z= 0.242 Angle : 0.713 6.540 46992 Z= 0.390 Chirality : 0.041 0.154 4896 Planarity : 0.004 0.024 6192 Dihedral : 4.611 22.744 4560 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 6.11 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.16 (0.13), residues: 4128 helix: 3.32 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.63 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 156 TYR 0.017 0.003 TYR C 137 PHE 0.021 0.003 PHE P 41 TRP 0.012 0.004 TRP Q 93 HIS 0.007 0.002 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (34920) covalent geometry : angle 0.71345 / 0.39 (46992) hydrogen bonds : bond 0.06018 / 4.02 ( 2640) hydrogen bonds : angle 3.99909 / 2.94 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 912 time to evaluate : 1.375 Fit side-chains REVERT: T 165 MET cc_start: 0.8370 (tpp) cc_final: 0.8138 (tpp) outliers start: 24 outliers final: 24 residues processed: 912 average time/residue: 1.0245 time to fit residues: 1061.3974 Evaluate side-chains 936 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 912 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 137 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 382 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.177635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.165223 restraints weight = 12583.732| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 0.26 r_work: 0.3712 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3268 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34920 Z= 0.226 Angle : 0.689 5.681 46992 Z= 0.377 Chirality : 0.040 0.147 4896 Planarity : 0.004 0.021 6192 Dihedral : 4.612 22.813 4560 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 6.06 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.13 (0.13), residues: 4128 helix: 3.30 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.62 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 156 TYR 0.017 0.003 TYR J 137 PHE 0.019 0.003 PHE V 41 TRP 0.013 0.004 TRP T 93 HIS 0.007 0.002 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (34920) covalent geometry : angle 0.68875 / 0.38 (46992) hydrogen bonds : bond 0.05852 / 3.92 ( 2640) hydrogen bonds : angle 3.96818 / 2.92 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29748.94 seconds wall clock time: 503 minutes 9.98 seconds (30189.98 seconds total)