Starting phenix.real_space_refine on Fri Sep 19 01:15:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn0_47022/09_2025/9dn0_47022.cif" } resolution = 3.1 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 7458 2.51 5 N 1749 2.21 5 O 1815 1.98 5 H 11088 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22176 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "D" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "E" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "F" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "H" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "I" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "J" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "K" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Time building chain proxies: 4.49, per 1000 atoms: 0.20 Number of scatterers: 22176 At special positions: 0 Unit cell: (143.061, 144.17, 52.123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1815 8.00 N 1749 7.00 C 7458 6.00 H 11088 1.00 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: 2.04 Conformation dependent library (CDL) restraints added in 580.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2596 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 1 sheets defined 76.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 54 through 103 removed outlier: 4.155A pdb=" N GLU A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 103 through 137 removed outlier: 3.840A pdb=" N ALA A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Proline residue: A 123 - end of helix removed outlier: 3.738A pdb=" N VAL A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 138 through 141 removed outlier: 3.647A pdb=" N SER A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 54 through 103 removed outlier: 4.150A pdb=" N GLU B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 103 through 137 removed outlier: 3.843A pdb=" N ALA B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix removed outlier: 3.725A pdb=" N VAL B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 138 through 141 removed outlier: 3.667A pdb=" N SER B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 54 through 103 removed outlier: 4.157A pdb=" N GLU C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 103 through 137 removed outlier: 3.846A pdb=" N ALA C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 3.734A pdb=" N VAL C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 138 through 141 removed outlier: 3.664A pdb=" N SER C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 54 through 103 removed outlier: 4.146A pdb=" N GLU D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 60 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Proline residue: D 82 - end of helix Processing helix chain 'D' and resid 103 through 137 removed outlier: 3.843A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 3.750A pdb=" N VAL D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Proline residue: D 131 - end of helix Processing helix chain 'D' and resid 138 through 141 removed outlier: 3.663A pdb=" N SER D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 54 through 103 removed outlier: 4.135A pdb=" N GLU E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 60 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Proline residue: E 82 - end of helix Processing helix chain 'E' and resid 103 through 137 removed outlier: 3.842A pdb=" N ALA E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Proline residue: E 123 - end of helix removed outlier: 3.738A pdb=" N VAL E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) Proline residue: E 131 - end of helix Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.661A pdb=" N SER E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 54 through 103 removed outlier: 4.153A pdb=" N GLU F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 60 " --> pdb=" O PHE F 56 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Proline residue: F 82 - end of helix Processing helix chain 'F' and resid 103 through 137 removed outlier: 3.836A pdb=" N ALA F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Proline residue: F 123 - end of helix removed outlier: 3.725A pdb=" N VAL F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Proline residue: F 131 - end of helix Processing helix chain 'F' and resid 138 through 141 removed outlier: 3.672A pdb=" N SER F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 54 through 103 removed outlier: 4.150A pdb=" N GLU G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 60 " --> pdb=" O PHE G 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Proline residue: G 82 - end of helix Processing helix chain 'G' and resid 103 through 137 removed outlier: 3.837A pdb=" N ALA G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Proline residue: G 123 - end of helix removed outlier: 3.743A pdb=" N VAL G 128 " --> pdb=" O ALA G 124 " (cutoff:3.500A) Proline residue: G 131 - end of helix Processing helix chain 'G' and resid 138 through 141 removed outlier: 3.666A pdb=" N SER G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 54 through 103 removed outlier: 4.165A pdb=" N GLU H 58 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 60 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 103 through 137 removed outlier: 3.836A pdb=" N ALA H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Proline residue: H 123 - end of helix removed outlier: 3.739A pdb=" N VAL H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Proline residue: H 131 - end of helix Processing helix chain 'H' and resid 138 through 141 removed outlier: 3.665A pdb=" N SER H 141 " --> pdb=" O LEU H 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 54 through 103 removed outlier: 4.152A pdb=" N GLU I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 60 " --> pdb=" O PHE I 56 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU I 76 " --> pdb=" O PHE I 72 " (cutoff:3.500A) Proline residue: I 82 - end of helix Processing helix chain 'I' and resid 103 through 137 removed outlier: 3.840A pdb=" N ALA I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Proline residue: I 123 - end of helix removed outlier: 3.733A pdb=" N VAL I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) Proline residue: I 131 - end of helix Processing helix chain 'I' and resid 138 through 141 removed outlier: 3.658A pdb=" N SER I 141 " --> pdb=" O LEU I 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 54 through 103 removed outlier: 4.154A pdb=" N GLU J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU J 76 " --> pdb=" O PHE J 72 " (cutoff:3.500A) Proline residue: J 82 - end of helix Processing helix chain 'J' and resid 103 through 137 removed outlier: 3.842A pdb=" N ALA J 120 " --> pdb=" O VAL J 116 " (cutoff:3.500A) Proline residue: J 123 - end of helix removed outlier: 3.737A pdb=" N VAL J 128 " --> pdb=" O ALA J 124 " (cutoff:3.500A) Proline residue: J 131 - end of helix Processing helix chain 'J' and resid 138 through 141 removed outlier: 3.666A pdb=" N SER J 141 " --> pdb=" O LEU J 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 54 through 103 removed outlier: 4.164A pdb=" N GLU K 58 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL K 60 " --> pdb=" O PHE K 56 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 76 " --> pdb=" O PHE K 72 " (cutoff:3.500A) Proline residue: K 82 - end of helix Processing helix chain 'K' and resid 103 through 137 removed outlier: 3.848A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Proline residue: K 123 - end of helix removed outlier: 3.730A pdb=" N VAL K 128 " --> pdb=" O ALA K 124 " (cutoff:3.500A) Proline residue: K 131 - end of helix Processing helix chain 'K' and resid 138 through 141 removed outlier: 3.657A pdb=" N SER K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 151 removed outlier: 6.900A pdb=" N LYS A 144 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N GLY D 145 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 146 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N PHE D 147 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 148 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N MET D 149 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN A 150 " --> pdb=" O MET D 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 143 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS B 144 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLY E 145 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN B 146 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE E 147 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS B 148 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N MET E 149 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 150 " --> pdb=" O MET E 149 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N SER E 151 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS E 144 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLY F 145 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN E 146 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE F 147 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS E 148 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N MET F 149 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN E 150 " --> pdb=" O MET F 149 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N SER F 151 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS F 144 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N GLY G 145 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN F 146 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE G 147 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 148 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET G 149 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN F 150 " --> pdb=" O MET G 149 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS G 144 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLY H 145 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN G 146 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE H 147 " --> pdb=" O GLN G 146 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS G 148 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS H 144 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY I 145 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN H 146 " --> pdb=" O GLY I 145 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N PHE I 147 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS H 148 " --> pdb=" O PHE I 147 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET I 149 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS I 144 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLY J 145 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN I 146 " --> pdb=" O GLY J 145 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N PHE J 147 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS I 148 " --> pdb=" O PHE J 147 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N MET J 149 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN I 150 " --> pdb=" O MET J 149 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS J 144 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLY K 145 " --> pdb=" O LYS J 144 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN J 146 " --> pdb=" O GLY K 145 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE K 147 " --> pdb=" O GLN J 146 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS J 148 " --> pdb=" O PHE K 147 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS K 148 " --> pdb=" O GLY A 145 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2118 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: 4.79 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11077 1.03 - 1.23: 11 1.23 - 1.42: 5137 1.42 - 1.62: 6193 1.62 - 1.81: 121 Bond restraints: 22539 Sorted by residual: bond pdb=" N ASP I 29 " pdb=" CA ASP I 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N ASP A 29 " pdb=" CA ASP A 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 bond pdb=" N ASP J 29 " pdb=" CA ASP J 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 bond pdb=" N ASP H 29 " pdb=" CA ASP H 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ASP F 29 " pdb=" CA ASP F 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 ... (remaining 22534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 36770 1.01 - 2.02: 3474 2.02 - 3.03: 236 3.03 - 4.03: 77 4.03 - 5.04: 22 Bond angle restraints: 40579 Sorted by residual: angle pdb=" C VAL E 100 " pdb=" N TRP E 101 " pdb=" CA TRP E 101 " ideal model delta sigma weight residual 122.60 119.50 3.10 1.56e+00 4.11e-01 3.95e+00 angle pdb=" C VAL I 100 " pdb=" N TRP I 101 " pdb=" CA TRP I 101 " ideal model delta sigma weight residual 122.60 119.57 3.03 1.56e+00 4.11e-01 3.76e+00 angle pdb=" C VAL H 100 " pdb=" N TRP H 101 " pdb=" CA TRP H 101 " ideal model delta sigma weight residual 122.60 119.58 3.02 1.56e+00 4.11e-01 3.75e+00 angle pdb=" C VAL F 100 " pdb=" N TRP F 101 " pdb=" CA TRP F 101 " ideal model delta sigma weight residual 122.60 119.60 3.00 1.56e+00 4.11e-01 3.69e+00 angle pdb=" C VAL B 100 " pdb=" N TRP B 101 " pdb=" CA TRP B 101 " ideal model delta sigma weight residual 122.60 119.61 2.99 1.56e+00 4.11e-01 3.67e+00 ... (remaining 40574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.82: 9463 12.82 - 25.64: 883 25.64 - 38.46: 237 38.46 - 51.29: 81 51.29 - 64.11: 94 Dihedral angle restraints: 10758 sinusoidal: 5390 harmonic: 5368 Sorted by residual: dihedral pdb=" CA MET E 52 " pdb=" C MET E 52 " pdb=" N GLY E 53 " pdb=" CA GLY E 53 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA MET F 52 " pdb=" C MET F 52 " pdb=" N GLY F 53 " pdb=" CA GLY F 53 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA MET H 52 " pdb=" C MET H 52 " pdb=" N GLY H 53 " pdb=" CA GLY H 53 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 10755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 955 0.027 - 0.054: 361 0.054 - 0.080: 257 0.080 - 0.107: 94 0.107 - 0.134: 27 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1691 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 104 " -0.015 5.00e-02 4.00e+02 2.32e-02 8.59e-01 pdb=" N PRO F 105 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 105 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 105 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 104 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO G 105 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO G 105 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 105 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 104 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.39e-01 pdb=" N PRO C 105 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " -0.013 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.45: 11294 2.45 - 2.99: 46799 2.99 - 3.52: 55218 3.52 - 4.06: 70249 4.06 - 4.60: 106394 Nonbonded interactions: 289954 Sorted by model distance: nonbonded pdb=" HD2 ARG F 32 " pdb="HH11 ARG F 32 " model vdw 1.911 2.270 nonbonded pdb=" OD1 ASN H 49 " pdb=" H ASN H 49 " model vdw 1.915 2.450 nonbonded pdb=" HD2 ARG B 32 " pdb="HH11 ARG B 32 " model vdw 1.925 2.270 nonbonded pdb=" HD2 ARG C 32 " pdb="HH11 ARG C 32 " model vdw 1.933 2.270 nonbonded pdb=" HB3 ARG D 32 " pdb=" HE ARG D 32 " model vdw 1.956 2.270 ... (remaining 289949 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 3.960 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: 0.150 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.600 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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: 0.020 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.003 0.034 11451 Z= 0.156 Angle : 0.581 5.043 15532 Z= 0.333 Chirality : 0.043 0.134 1694 Planarity : 0.004 0.023 1903 Dihedral : 12.715 59.467 3938 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1342 helix: 1.03 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 32 TYR 0.010 0.001 TYR H 121 PHE 0.011 0.001 PHE A 97 TRP 0.007 0.001 TRP B 113 HIS 0.002 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00268 (11451) covalent geometry : angle 0.58074 (15532) hydrogen bonds : bond 0.12735 ( 708) hydrogen bonds : angle 5.82598 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.612 Fit side-chains REVERT: A 32 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7845 (ttp80) REVERT: C 52 MET cc_start: 0.8236 (mtm) cc_final: 0.7742 (mtt) REVERT: C 134 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7729 (mtm-85) REVERT: D 43 ASP cc_start: 0.8687 (m-30) cc_final: 0.8416 (m-30) REVERT: D 134 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7770 (mtm-85) REVERT: E 134 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7835 (mtm-85) REVERT: G 134 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7840 (mtm-85) REVERT: H 43 ASP cc_start: 0.8562 (m-30) cc_final: 0.8267 (m-30) REVERT: I 32 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7880 (ttp80) REVERT: I 149 MET cc_start: 0.7763 (mmt) cc_final: 0.7165 (mmt) REVERT: J 52 MET cc_start: 0.8124 (mtt) cc_final: 0.7855 (mtp) REVERT: J 134 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7844 (mtm-85) REVERT: K 107 MET cc_start: 0.7988 (mmp) cc_final: 0.7435 (mmt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3865 time to fit residues: 80.8022 Evaluate side-chains 163 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 ASN K 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110985 restraints weight = 34955.069| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.84 r_work: 0.3124 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11451 Z= 0.127 Angle : 0.524 4.283 15532 Z= 0.292 Chirality : 0.041 0.136 1694 Planarity : 0.004 0.023 1903 Dihedral : 4.621 15.672 1474 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.19 % Allowed : 5.78 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1342 helix: 1.34 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 32 TYR 0.011 0.001 TYR F 110 PHE 0.011 0.001 PHE F 45 TRP 0.007 0.001 TRP G 101 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00279 (11451) covalent geometry : angle 0.52437 (15532) hydrogen bonds : bond 0.06313 ( 708) hydrogen bonds : angle 4.64710 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.606 Fit side-chains REVERT: A 32 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7753 (ttp80) REVERT: A 107 MET cc_start: 0.7959 (mmt) cc_final: 0.7376 (mmt) REVERT: A 149 MET cc_start: 0.7923 (mmt) cc_final: 0.7648 (mmt) REVERT: C 52 MET cc_start: 0.8187 (mtm) cc_final: 0.7728 (mtt) REVERT: C 134 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7479 (mtm-85) REVERT: D 43 ASP cc_start: 0.8650 (m-30) cc_final: 0.8375 (m-30) REVERT: D 134 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7740 (mtm-85) REVERT: E 43 ASP cc_start: 0.8695 (m-30) cc_final: 0.8358 (m-30) REVERT: E 134 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7792 (mtm-85) REVERT: G 134 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7728 (mtm-85) REVERT: H 43 ASP cc_start: 0.8553 (m-30) cc_final: 0.8247 (m-30) REVERT: I 32 ARG cc_start: 0.8302 (ttp-170) cc_final: 0.7834 (ttp80) REVERT: I 52 MET cc_start: 0.8201 (mtp) cc_final: 0.7721 (mtt) REVERT: I 149 MET cc_start: 0.7738 (mmt) cc_final: 0.7162 (mmt) REVERT: J 52 MET cc_start: 0.8183 (mtt) cc_final: 0.7917 (mtp) REVERT: J 134 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7603 (mtm-85) REVERT: K 32 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8176 (ttp-170) outliers start: 14 outliers final: 5 residues processed: 183 average time/residue: 0.3670 time to fit residues: 86.4366 Evaluate side-chains 165 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108320 restraints weight = 35532.206| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.91 r_work: 0.3075 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11451 Z= 0.135 Angle : 0.516 4.184 15532 Z= 0.287 Chirality : 0.040 0.135 1694 Planarity : 0.004 0.024 1903 Dihedral : 4.399 14.901 1474 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.36 % Allowed : 5.78 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1342 helix: 1.37 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.09 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 126 TYR 0.010 0.001 TYR F 110 PHE 0.009 0.001 PHE C 88 TRP 0.004 0.001 TRP G 101 HIS 0.003 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00296 (11451) covalent geometry : angle 0.51582 (15532) hydrogen bonds : bond 0.06950 ( 708) hydrogen bonds : angle 4.67058 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.640 Fit side-chains REVERT: A 32 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7812 (ttp80) REVERT: A 66 LYS cc_start: 0.8110 (tttt) cc_final: 0.7823 (ttpp) REVERT: A 107 MET cc_start: 0.8022 (mmt) cc_final: 0.7432 (mmt) REVERT: A 149 MET cc_start: 0.7919 (mmt) cc_final: 0.7642 (mmt) REVERT: C 52 MET cc_start: 0.8212 (mtm) cc_final: 0.7760 (mtt) REVERT: C 134 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7544 (mtm-85) REVERT: D 43 ASP cc_start: 0.8630 (m-30) cc_final: 0.8338 (m-30) REVERT: D 134 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7881 (mtm-85) REVERT: E 43 ASP cc_start: 0.8730 (m-30) cc_final: 0.8454 (m-30) REVERT: E 134 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7816 (mtm-85) REVERT: G 66 LYS cc_start: 0.7900 (tttt) cc_final: 0.7516 (ttpp) REVERT: G 134 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7708 (mtm-85) REVERT: H 43 ASP cc_start: 0.8639 (m-30) cc_final: 0.8361 (m-30) REVERT: I 32 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7684 (ttp80) REVERT: I 52 MET cc_start: 0.8210 (mtp) cc_final: 0.7720 (mtt) REVERT: I 91 SER cc_start: 0.8413 (t) cc_final: 0.8192 (m) REVERT: I 107 MET cc_start: 0.8204 (mmt) cc_final: 0.7656 (mmt) REVERT: I 149 MET cc_start: 0.7666 (mmt) cc_final: 0.7072 (mmt) REVERT: J 134 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7816 (mtm-85) REVERT: K 32 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8231 (ttp-170) outliers start: 16 outliers final: 16 residues processed: 182 average time/residue: 0.4061 time to fit residues: 93.2816 Evaluate side-chains 165 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099874 restraints weight = 36431.206| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.92 r_work: 0.3009 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11451 Z= 0.195 Angle : 0.567 4.385 15532 Z= 0.320 Chirality : 0.042 0.135 1694 Planarity : 0.004 0.025 1903 Dihedral : 4.451 14.807 1474 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.61 % Allowed : 6.03 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1342 helix: 1.12 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.27 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 115 TYR 0.013 0.002 TYR C 110 PHE 0.010 0.001 PHE C 88 TRP 0.007 0.001 TRP G 101 HIS 0.003 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00476 (11451) covalent geometry : angle 0.56676 (15532) hydrogen bonds : bond 0.08203 ( 708) hydrogen bonds : angle 4.77290 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.575 Fit side-chains REVERT: A 32 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.7778 (ttp80) REVERT: A 66 LYS cc_start: 0.8259 (tttt) cc_final: 0.7962 (ttpp) REVERT: A 149 MET cc_start: 0.7879 (mmt) cc_final: 0.7643 (mmt) REVERT: B 66 LYS cc_start: 0.8293 (tttt) cc_final: 0.7990 (ttpp) REVERT: B 91 SER cc_start: 0.8507 (t) cc_final: 0.8226 (m) REVERT: C 52 MET cc_start: 0.8213 (mtm) cc_final: 0.7761 (mtt) REVERT: C 134 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7560 (mtm-85) REVERT: D 43 ASP cc_start: 0.8615 (m-30) cc_final: 0.8357 (m-30) REVERT: D 91 SER cc_start: 0.8418 (t) cc_final: 0.8117 (m) REVERT: D 134 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7806 (mtm-85) REVERT: E 43 ASP cc_start: 0.8705 (m-30) cc_final: 0.8405 (m-30) REVERT: E 66 LYS cc_start: 0.8092 (tttt) cc_final: 0.7807 (ttpt) REVERT: E 91 SER cc_start: 0.8539 (t) cc_final: 0.8228 (m) REVERT: E 134 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7863 (mtm-85) REVERT: F 66 LYS cc_start: 0.8203 (tttt) cc_final: 0.7861 (ttpp) REVERT: F 134 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7642 (mtm-85) REVERT: G 66 LYS cc_start: 0.8079 (tttt) cc_final: 0.7729 (ttpp) REVERT: G 134 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7727 (mtm-85) REVERT: H 43 ASP cc_start: 0.8574 (m-30) cc_final: 0.8315 (m-30) REVERT: H 66 LYS cc_start: 0.8221 (tttt) cc_final: 0.7895 (ttpt) REVERT: H 91 SER cc_start: 0.8334 (t) cc_final: 0.8096 (m) REVERT: I 32 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7779 (ttp80) REVERT: I 52 MET cc_start: 0.8204 (mtp) cc_final: 0.7697 (mtt) REVERT: I 66 LYS cc_start: 0.8047 (tttt) cc_final: 0.7720 (ttpt) REVERT: I 91 SER cc_start: 0.8563 (t) cc_final: 0.8228 (m) REVERT: I 107 MET cc_start: 0.8267 (mmt) cc_final: 0.7748 (mmt) REVERT: I 149 MET cc_start: 0.7635 (mmt) cc_final: 0.7062 (mmt) REVERT: J 66 LYS cc_start: 0.8074 (tttt) cc_final: 0.7747 (ttpp) REVERT: J 134 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7800 (mtm-85) REVERT: K 32 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8241 (ttp-170) REVERT: K 66 LYS cc_start: 0.8226 (tttt) cc_final: 0.7914 (ttpp) REVERT: K 107 MET cc_start: 0.8199 (mmp) cc_final: 0.7704 (mmt) REVERT: K 134 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7721 (mtm-85) outliers start: 19 outliers final: 19 residues processed: 179 average time/residue: 0.3756 time to fit residues: 85.8827 Evaluate side-chains 178 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 38 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106015 restraints weight = 35527.200| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.88 r_work: 0.3062 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11451 Z= 0.131 Angle : 0.507 4.060 15532 Z= 0.283 Chirality : 0.040 0.131 1694 Planarity : 0.004 0.025 1903 Dihedral : 4.394 14.852 1474 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.85 % Allowed : 7.05 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.23), residues: 1342 helix: 1.29 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.009 0.001 TYR K 110 PHE 0.008 0.001 PHE H 97 TRP 0.005 0.001 TRP G 101 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00287 (11451) covalent geometry : angle 0.50684 (15532) hydrogen bonds : bond 0.06640 ( 708) hydrogen bonds : angle 4.54413 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.618 Fit side-chains REVERT: A 32 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7741 (ttp80) REVERT: A 66 LYS cc_start: 0.8168 (tttt) cc_final: 0.7876 (ttpp) REVERT: A 107 MET cc_start: 0.7939 (mmt) cc_final: 0.7299 (mmt) REVERT: A 149 MET cc_start: 0.7911 (mmt) cc_final: 0.7679 (mmt) REVERT: B 66 LYS cc_start: 0.8288 (tttt) cc_final: 0.7992 (ttpp) REVERT: B 91 SER cc_start: 0.8428 (t) cc_final: 0.8162 (m) REVERT: C 52 MET cc_start: 0.8205 (mtm) cc_final: 0.7743 (mtt) REVERT: C 134 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7496 (mtm-85) REVERT: D 43 ASP cc_start: 0.8601 (m-30) cc_final: 0.8325 (m-30) REVERT: D 91 SER cc_start: 0.8319 (t) cc_final: 0.8038 (m) REVERT: D 134 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7724 (mtm-85) REVERT: E 43 ASP cc_start: 0.8656 (m-30) cc_final: 0.8410 (m-30) REVERT: E 52 MET cc_start: 0.8173 (mtp) cc_final: 0.7596 (mtt) REVERT: E 66 LYS cc_start: 0.8031 (tttt) cc_final: 0.7751 (ttpt) REVERT: E 134 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7727 (mtm-85) REVERT: F 134 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7521 (mtm-85) REVERT: G 66 LYS cc_start: 0.8036 (tttt) cc_final: 0.7788 (ttpp) REVERT: G 134 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7672 (mtm-85) REVERT: H 43 ASP cc_start: 0.8621 (m-30) cc_final: 0.8347 (m-30) REVERT: H 52 MET cc_start: 0.8319 (mtp) cc_final: 0.7797 (mtt) REVERT: H 91 SER cc_start: 0.8248 (t) cc_final: 0.8033 (m) REVERT: I 32 ARG cc_start: 0.8309 (ttp-170) cc_final: 0.7739 (ttp80) REVERT: I 52 MET cc_start: 0.8163 (mtp) cc_final: 0.7638 (mtt) REVERT: I 91 SER cc_start: 0.8457 (t) cc_final: 0.8142 (m) REVERT: I 107 MET cc_start: 0.8179 (mmt) cc_final: 0.7627 (mmt) REVERT: I 149 MET cc_start: 0.7582 (mmt) cc_final: 0.7045 (mmt) REVERT: J 66 LYS cc_start: 0.8017 (tttt) cc_final: 0.7719 (ttpp) REVERT: J 134 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7789 (mtm-85) REVERT: K 32 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8188 (ttp-170) REVERT: K 107 MET cc_start: 0.8142 (mmp) cc_final: 0.7664 (mmt) REVERT: K 134 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7617 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 163 average time/residue: 0.3905 time to fit residues: 80.6124 Evaluate side-chains 162 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103274 restraints weight = 36420.293| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.93 r_work: 0.2995 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11451 Z= 0.204 Angle : 0.565 4.305 15532 Z= 0.318 Chirality : 0.042 0.133 1694 Planarity : 0.004 0.024 1903 Dihedral : 4.394 14.676 1474 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.27 % Allowed : 7.31 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.22), residues: 1342 helix: 1.08 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.29 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 115 TYR 0.013 0.002 TYR C 110 PHE 0.011 0.001 PHE C 88 TRP 0.007 0.001 TRP G 101 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00499 (11451) covalent geometry : angle 0.56466 (15532) hydrogen bonds : bond 0.08219 ( 708) hydrogen bonds : angle 4.73842 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.467 Fit side-chains REVERT: A 32 ARG cc_start: 0.8450 (ttp-170) cc_final: 0.7782 (ttp80) REVERT: A 66 LYS cc_start: 0.8234 (tttt) cc_final: 0.7931 (ttpp) REVERT: A 149 MET cc_start: 0.7902 (mmt) cc_final: 0.7669 (mmt) REVERT: B 66 LYS cc_start: 0.8307 (tttt) cc_final: 0.7928 (ttpt) REVERT: B 91 SER cc_start: 0.8520 (t) cc_final: 0.8211 (m) REVERT: C 52 MET cc_start: 0.8193 (mtm) cc_final: 0.7740 (mtt) REVERT: C 134 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7536 (mtm-85) REVERT: D 43 ASP cc_start: 0.8645 (m-30) cc_final: 0.8401 (m-30) REVERT: D 91 SER cc_start: 0.8362 (t) cc_final: 0.8097 (m) REVERT: D 134 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7716 (mtm-85) REVERT: E 43 ASP cc_start: 0.8671 (m-30) cc_final: 0.8358 (m-30) REVERT: E 66 LYS cc_start: 0.8072 (tttt) cc_final: 0.7770 (ttpt) REVERT: E 91 SER cc_start: 0.8552 (t) cc_final: 0.8238 (m) REVERT: E 134 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7863 (mtm-85) REVERT: F 66 LYS cc_start: 0.8210 (tttt) cc_final: 0.7849 (ttpp) REVERT: F 134 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7619 (mtm-85) REVERT: G 66 LYS cc_start: 0.8102 (tttt) cc_final: 0.7784 (ttpp) REVERT: G 134 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7694 (mtm-85) REVERT: H 43 ASP cc_start: 0.8614 (m-30) cc_final: 0.8359 (m-30) REVERT: H 52 MET cc_start: 0.8341 (mtp) cc_final: 0.7816 (mtt) REVERT: H 66 LYS cc_start: 0.8238 (tttt) cc_final: 0.7909 (ttpt) REVERT: H 91 SER cc_start: 0.8367 (t) cc_final: 0.8091 (m) REVERT: I 52 MET cc_start: 0.8177 (mtp) cc_final: 0.7663 (mtt) REVERT: I 66 LYS cc_start: 0.7995 (tttt) cc_final: 0.7693 (ttpt) REVERT: I 91 SER cc_start: 0.8601 (t) cc_final: 0.8255 (m) REVERT: I 149 MET cc_start: 0.7545 (mmt) cc_final: 0.7050 (mmt) REVERT: J 52 MET cc_start: 0.8108 (mtt) cc_final: 0.7843 (mtp) REVERT: J 66 LYS cc_start: 0.8229 (tttt) cc_final: 0.7906 (ttpp) REVERT: J 134 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7796 (mtm-85) REVERT: K 32 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8232 (ttp-170) REVERT: K 66 LYS cc_start: 0.8236 (tttt) cc_final: 0.7917 (ttpp) REVERT: K 107 MET cc_start: 0.8182 (mmp) cc_final: 0.7658 (mmt) REVERT: K 134 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7687 (mtm-85) outliers start: 15 outliers final: 15 residues processed: 175 average time/residue: 0.3933 time to fit residues: 86.8016 Evaluate side-chains 174 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105184 restraints weight = 36039.696| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.91 r_work: 0.3041 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11451 Z= 0.147 Angle : 0.521 4.070 15532 Z= 0.292 Chirality : 0.041 0.132 1694 Planarity : 0.004 0.025 1903 Dihedral : 4.376 14.697 1474 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.93 % Allowed : 7.65 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.22), residues: 1342 helix: 1.18 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.010 0.001 TYR K 110 PHE 0.008 0.001 PHE C 88 TRP 0.006 0.001 TRP G 101 HIS 0.003 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00334 (11451) covalent geometry : angle 0.52116 (15532) hydrogen bonds : bond 0.07075 ( 708) hydrogen bonds : angle 4.58440 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.599 Fit side-chains REVERT: A 32 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7797 (ttp80) REVERT: A 66 LYS cc_start: 0.8144 (tttt) cc_final: 0.7831 (ttpp) REVERT: A 107 MET cc_start: 0.8028 (mmt) cc_final: 0.7394 (mmt) REVERT: A 149 MET cc_start: 0.7885 (mmt) cc_final: 0.7669 (mmt) REVERT: B 66 LYS cc_start: 0.8268 (tttt) cc_final: 0.7951 (ttpp) REVERT: B 91 SER cc_start: 0.8475 (t) cc_final: 0.8174 (m) REVERT: C 52 MET cc_start: 0.8200 (mtm) cc_final: 0.7747 (mtt) REVERT: C 134 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7513 (mtm-85) REVERT: D 43 ASP cc_start: 0.8585 (m-30) cc_final: 0.8324 (m-30) REVERT: D 91 SER cc_start: 0.8350 (t) cc_final: 0.8073 (m) REVERT: D 134 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7667 (mtm-85) REVERT: D 149 MET cc_start: 0.7713 (mmt) cc_final: 0.7190 (mmt) REVERT: E 43 ASP cc_start: 0.8689 (m-30) cc_final: 0.8443 (m-30) REVERT: E 66 LYS cc_start: 0.8069 (tttt) cc_final: 0.7776 (ttpt) REVERT: E 134 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7768 (mtm-85) REVERT: F 52 MET cc_start: 0.8180 (mtp) cc_final: 0.7731 (mtt) REVERT: F 66 LYS cc_start: 0.8151 (tttt) cc_final: 0.7784 (ttpp) REVERT: F 134 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7562 (mtm-85) REVERT: G 66 LYS cc_start: 0.8064 (tttt) cc_final: 0.7780 (ttpp) REVERT: G 134 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7658 (mtm-85) REVERT: H 43 ASP cc_start: 0.8612 (m-30) cc_final: 0.8352 (m-30) REVERT: H 52 MET cc_start: 0.8311 (mtp) cc_final: 0.7776 (mtt) REVERT: H 66 LYS cc_start: 0.8210 (tttt) cc_final: 0.7879 (ttpt) REVERT: H 91 SER cc_start: 0.8310 (t) cc_final: 0.8053 (m) REVERT: I 52 MET cc_start: 0.8163 (mtp) cc_final: 0.7641 (mtt) REVERT: I 66 LYS cc_start: 0.7936 (tttt) cc_final: 0.7651 (ttpt) REVERT: I 91 SER cc_start: 0.8506 (t) cc_final: 0.8152 (m) REVERT: I 149 MET cc_start: 0.7502 (mmt) cc_final: 0.7024 (mmt) REVERT: J 52 MET cc_start: 0.8086 (mtt) cc_final: 0.7860 (mtp) REVERT: J 66 LYS cc_start: 0.8126 (tttt) cc_final: 0.7820 (ttpp) REVERT: J 134 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7761 (mtm-85) REVERT: K 32 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: K 66 LYS cc_start: 0.8188 (tttt) cc_final: 0.7878 (ttpp) REVERT: K 107 MET cc_start: 0.8172 (mmp) cc_final: 0.7692 (mmt) REVERT: K 134 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7611 (mtm-85) outliers start: 11 outliers final: 11 residues processed: 169 average time/residue: 0.4033 time to fit residues: 85.7255 Evaluate side-chains 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107507 restraints weight = 35940.960| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.91 r_work: 0.3116 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11451 Z= 0.104 Angle : 0.478 3.848 15532 Z= 0.264 Chirality : 0.040 0.127 1694 Planarity : 0.003 0.026 1903 Dihedral : 4.272 15.253 1474 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.93 % Allowed : 7.65 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.23), residues: 1342 helix: 1.54 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.97 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 32 TYR 0.007 0.001 TYR G 110 PHE 0.007 0.001 PHE I 45 TRP 0.005 0.001 TRP G 101 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00205 (11451) covalent geometry : angle 0.47798 (15532) hydrogen bonds : bond 0.05454 ( 708) hydrogen bonds : angle 4.36420 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.723 Fit side-chains REVERT: A 32 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.7737 (ttp80) REVERT: A 66 LYS cc_start: 0.8069 (tttt) cc_final: 0.7767 (ttpp) REVERT: A 107 MET cc_start: 0.7940 (mmt) cc_final: 0.7281 (mmt) REVERT: A 149 MET cc_start: 0.7839 (mmt) cc_final: 0.7628 (mmt) REVERT: B 66 LYS cc_start: 0.8293 (tttt) cc_final: 0.8006 (ttpp) REVERT: B 91 SER cc_start: 0.8449 (t) cc_final: 0.8190 (m) REVERT: B 149 MET cc_start: 0.7596 (mmt) cc_final: 0.6913 (mmt) REVERT: C 52 MET cc_start: 0.8152 (mtm) cc_final: 0.7708 (mtt) REVERT: C 134 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7474 (mtm-85) REVERT: D 43 ASP cc_start: 0.8586 (m-30) cc_final: 0.8327 (m-30) REVERT: D 52 MET cc_start: 0.8220 (mtp) cc_final: 0.7592 (mtt) REVERT: D 91 SER cc_start: 0.8294 (t) cc_final: 0.8087 (m) REVERT: D 134 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7677 (mtm-85) REVERT: D 149 MET cc_start: 0.7650 (mmt) cc_final: 0.7208 (mmt) REVERT: E 43 ASP cc_start: 0.8704 (m-30) cc_final: 0.8411 (m-30) REVERT: E 52 MET cc_start: 0.8093 (mtp) cc_final: 0.7532 (mtt) REVERT: E 66 LYS cc_start: 0.8050 (tttt) cc_final: 0.7775 (ttpt) REVERT: E 113 TRP cc_start: 0.7931 (m100) cc_final: 0.7578 (m100) REVERT: E 134 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7824 (mtm-85) REVERT: F 52 MET cc_start: 0.8132 (mtp) cc_final: 0.7673 (mtt) REVERT: G 66 LYS cc_start: 0.8018 (tttt) cc_final: 0.7779 (ttpp) REVERT: G 134 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7604 (mtm-85) REVERT: H 43 ASP cc_start: 0.8668 (m-30) cc_final: 0.8401 (m-30) REVERT: H 52 MET cc_start: 0.8251 (mtp) cc_final: 0.7646 (mtt) REVERT: I 52 MET cc_start: 0.8194 (mtp) cc_final: 0.7685 (mtt) REVERT: I 91 SER cc_start: 0.8374 (t) cc_final: 0.8117 (m) REVERT: I 149 MET cc_start: 0.7522 (mmt) cc_final: 0.7033 (mmt) REVERT: J 52 MET cc_start: 0.8147 (mtt) cc_final: 0.7901 (mtp) REVERT: J 66 LYS cc_start: 0.7983 (tttt) cc_final: 0.7685 (ttpp) REVERT: J 134 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7750 (mtm-85) REVERT: K 32 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8170 (ttp-170) REVERT: K 107 MET cc_start: 0.8111 (mmp) cc_final: 0.7645 (mmt) REVERT: K 134 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7674 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 167 average time/residue: 0.3815 time to fit residues: 81.2426 Evaluate side-chains 163 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108608 restraints weight = 35893.985| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.90 r_work: 0.3083 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11451 Z= 0.119 Angle : 0.490 3.966 15532 Z= 0.272 Chirality : 0.040 0.128 1694 Planarity : 0.003 0.024 1903 Dihedral : 4.190 14.833 1474 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.85 % Allowed : 7.90 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.23), residues: 1342 helix: 1.50 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.009 0.001 TYR F 110 PHE 0.008 0.001 PHE C 88 TRP 0.004 0.001 TRP G 101 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00253 (11451) covalent geometry : angle 0.48981 (15532) hydrogen bonds : bond 0.06187 ( 708) hydrogen bonds : angle 4.45163 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.622 Fit side-chains REVERT: A 32 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.7736 (ttp80) REVERT: A 66 LYS cc_start: 0.8078 (tttt) cc_final: 0.7779 (ttpp) REVERT: A 107 MET cc_start: 0.8021 (mmt) cc_final: 0.7387 (mmt) REVERT: B 66 LYS cc_start: 0.8313 (tttt) cc_final: 0.8034 (ttpp) REVERT: B 91 SER cc_start: 0.8492 (t) cc_final: 0.8201 (m) REVERT: B 149 MET cc_start: 0.7587 (mmt) cc_final: 0.6899 (mmt) REVERT: C 52 MET cc_start: 0.8139 (mtm) cc_final: 0.7689 (mtt) REVERT: C 134 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7456 (mtm-85) REVERT: D 43 ASP cc_start: 0.8558 (m-30) cc_final: 0.8294 (m-30) REVERT: D 52 MET cc_start: 0.8224 (mtp) cc_final: 0.7596 (mtt) REVERT: D 91 SER cc_start: 0.8347 (t) cc_final: 0.8110 (m) REVERT: D 134 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7709 (mtm-85) REVERT: D 149 MET cc_start: 0.7726 (mmt) cc_final: 0.7272 (mmt) REVERT: E 43 ASP cc_start: 0.8685 (m-30) cc_final: 0.8442 (m-30) REVERT: E 52 MET cc_start: 0.8086 (mtp) cc_final: 0.7541 (mtt) REVERT: E 66 LYS cc_start: 0.8060 (tttt) cc_final: 0.7791 (ttpp) REVERT: E 113 TRP cc_start: 0.7956 (m100) cc_final: 0.7599 (m100) REVERT: E 134 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7839 (mtm-85) REVERT: F 52 MET cc_start: 0.8115 (mtp) cc_final: 0.7654 (mtt) REVERT: G 66 LYS cc_start: 0.8006 (tttt) cc_final: 0.7752 (ttpp) REVERT: G 134 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7537 (mtm-85) REVERT: H 43 ASP cc_start: 0.8674 (m-30) cc_final: 0.8410 (m-30) REVERT: H 52 MET cc_start: 0.8281 (mtp) cc_final: 0.7665 (mtt) REVERT: I 52 MET cc_start: 0.8162 (mtp) cc_final: 0.7658 (mtt) REVERT: I 66 LYS cc_start: 0.7940 (tttt) cc_final: 0.7674 (ttpt) REVERT: I 91 SER cc_start: 0.8432 (t) cc_final: 0.8140 (m) REVERT: I 107 MET cc_start: 0.8299 (mmt) cc_final: 0.7771 (mmt) REVERT: I 149 MET cc_start: 0.7444 (mmt) cc_final: 0.6943 (mmt) REVERT: J 52 MET cc_start: 0.8136 (mtt) cc_final: 0.7901 (mtp) REVERT: J 66 LYS cc_start: 0.8073 (tttt) cc_final: 0.7784 (ttpp) REVERT: J 134 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7774 (mtm-85) REVERT: K 32 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8189 (ttp-170) REVERT: K 107 MET cc_start: 0.8174 (mmp) cc_final: 0.7737 (mmt) REVERT: K 134 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7695 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 161 average time/residue: 0.3734 time to fit residues: 76.8413 Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105416 restraints weight = 36094.259| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.92 r_work: 0.3065 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11451 Z= 0.127 Angle : 0.501 4.014 15532 Z= 0.278 Chirality : 0.040 0.129 1694 Planarity : 0.003 0.024 1903 Dihedral : 4.200 14.837 1474 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.93 % Allowed : 7.82 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.23), residues: 1342 helix: 1.45 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.009 0.001 TYR D 110 PHE 0.008 0.001 PHE C 88 TRP 0.005 0.001 TRP G 101 HIS 0.003 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00278 (11451) covalent geometry : angle 0.50055 (15532) hydrogen bonds : bond 0.06475 ( 708) hydrogen bonds : angle 4.47081 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.654 Fit side-chains REVERT: A 32 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.7726 (ttp80) REVERT: A 66 LYS cc_start: 0.8051 (tttt) cc_final: 0.7751 (ttpp) REVERT: A 107 MET cc_start: 0.8022 (mmt) cc_final: 0.7382 (mmt) REVERT: B 66 LYS cc_start: 0.8245 (tttt) cc_final: 0.7954 (ttpp) REVERT: B 91 SER cc_start: 0.8446 (t) cc_final: 0.8171 (m) REVERT: B 149 MET cc_start: 0.7532 (mmt) cc_final: 0.6861 (mmt) REVERT: C 52 MET cc_start: 0.8137 (mtm) cc_final: 0.7676 (mtt) REVERT: C 134 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7454 (mtm-85) REVERT: D 43 ASP cc_start: 0.8564 (m-30) cc_final: 0.8302 (m-30) REVERT: D 52 MET cc_start: 0.8203 (mtp) cc_final: 0.7570 (mtt) REVERT: D 91 SER cc_start: 0.8320 (t) cc_final: 0.8064 (m) REVERT: D 134 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7695 (mtm-85) REVERT: D 149 MET cc_start: 0.7724 (mmt) cc_final: 0.7330 (mmt) REVERT: E 43 ASP cc_start: 0.8658 (m-30) cc_final: 0.8415 (m-30) REVERT: E 52 MET cc_start: 0.8084 (mtp) cc_final: 0.7509 (mtt) REVERT: E 66 LYS cc_start: 0.8045 (tttt) cc_final: 0.7766 (ttpp) REVERT: E 113 TRP cc_start: 0.7981 (m100) cc_final: 0.7617 (m100) REVERT: E 134 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7820 (mtm-85) REVERT: F 52 MET cc_start: 0.8091 (mtp) cc_final: 0.7614 (mtt) REVERT: F 66 LYS cc_start: 0.8104 (tttt) cc_final: 0.7807 (ttpp) REVERT: G 66 LYS cc_start: 0.8049 (tttt) cc_final: 0.7807 (ttpp) REVERT: G 134 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7517 (mtm-85) REVERT: H 43 ASP cc_start: 0.8685 (m-30) cc_final: 0.8415 (m-30) REVERT: H 49 ASN cc_start: 0.8376 (m110) cc_final: 0.8158 (m110) REVERT: H 52 MET cc_start: 0.8297 (mtp) cc_final: 0.7671 (mtt) REVERT: H 66 LYS cc_start: 0.8177 (tttt) cc_final: 0.7948 (ttpp) REVERT: I 52 MET cc_start: 0.8114 (mtp) cc_final: 0.7599 (mtt) REVERT: I 66 LYS cc_start: 0.7901 (tttt) cc_final: 0.7636 (ttpt) REVERT: I 91 SER cc_start: 0.8443 (t) cc_final: 0.8134 (m) REVERT: I 107 MET cc_start: 0.8254 (mmt) cc_final: 0.7711 (mmt) REVERT: I 149 MET cc_start: 0.7401 (mmt) cc_final: 0.6917 (mmt) REVERT: J 66 LYS cc_start: 0.8060 (tttt) cc_final: 0.7750 (ttpp) REVERT: J 134 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7761 (mtm-85) REVERT: K 32 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8182 (ttp-170) REVERT: K 107 MET cc_start: 0.8148 (mmp) cc_final: 0.7699 (mmt) REVERT: K 134 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7675 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 163 average time/residue: 0.3918 time to fit residues: 80.9124 Evaluate side-chains 163 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105555 restraints weight = 35895.126| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.87 r_work: 0.3087 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11451 Z= 0.117 Angle : 0.491 3.960 15532 Z= 0.272 Chirality : 0.040 0.128 1694 Planarity : 0.003 0.024 1903 Dihedral : 4.189 14.916 1474 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.85 % Allowed : 8.07 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.23), residues: 1342 helix: 1.51 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.93 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.009 0.001 TYR A 110 PHE 0.007 0.001 PHE F 45 TRP 0.005 0.001 TRP G 101 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00248 (11451) covalent geometry : angle 0.49118 (15532) hydrogen bonds : bond 0.06110 ( 708) hydrogen bonds : angle 4.42300 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.50 seconds wall clock time: 85 minutes 43.40 seconds (5143.40 seconds total)