Starting phenix.real_space_refine on Thu Sep 18 20:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1j_61073/09_2025/9j1j_61073.cif" } resolution = 3.42 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= 0.053 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12630 2.51 5 N 3264 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s 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: 19944 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "g" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "B" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "C" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "D" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "E" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "H" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "I" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "K" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "L" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "M" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "N" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "O" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "P" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "Q" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1088 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Time building chain proxies: 4.96, per 1000 atoms: 0.25 Number of scatterers: 19944 At special positions: 0 Unit cell: (106.346, 109.568, 145.017, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3924 8.00 N 3264 7.00 C 12630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS g 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS K 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 9 " - pdb=" SG CYS Q 104 " distance=2.03 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: 1.79 Conformation dependent library (CDL) restraints added in 965.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 14.8% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.709A pdb=" N ALA G 94 " --> pdb=" O HIS G 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 22 No H-bonds generated for 'chain 'g' and resid 20 through 22' Processing helix chain 'g' and resid 89 through 100 removed outlier: 4.101A pdb=" N LYS g 95 " --> pdb=" O LYS g 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 21 removed outlier: 3.670A pdb=" N VAL F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.704A pdb=" N VAL F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 21 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.684A pdb=" N VAL A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 87 through 100 removed outlier: 4.304A pdb=" N LYS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 89 through 100 removed outlier: 3.525A pdb=" N ALA C 94 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 22 Processing helix chain 'D' and resid 71 through 84 removed outlier: 3.810A pdb=" N GLY D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.736A pdb=" N ALA E 94 " --> pdb=" O HIS E 90 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.715A pdb=" N ALA H 94 " --> pdb=" O HIS H 90 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS H 95 " --> pdb=" O LYS H 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 22 removed outlier: 3.753A pdb=" N VAL I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.640A pdb=" N VAL I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 22 No H-bonds generated for 'chain 'J' and resid 20 through 22' Processing helix chain 'J' and resid 89 through 100 removed outlier: 3.703A pdb=" N ALA J 94 " --> pdb=" O HIS J 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS J 95 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 22 No H-bonds generated for 'chain 'K' and resid 20 through 22' Processing helix chain 'K' and resid 87 through 100 removed outlier: 3.672A pdb=" N ALA K 94 " --> pdb=" O HIS K 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS K 95 " --> pdb=" O LYS K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.725A pdb=" N VAL L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 87 through 100 removed outlier: 3.526A pdb=" N ALA M 94 " --> pdb=" O HIS M 90 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS M 95 " --> pdb=" O LYS M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 22 No H-bonds generated for 'chain 'N' and resid 20 through 22' Processing helix chain 'N' and resid 87 through 100 removed outlier: 3.599A pdb=" N ALA N 94 " --> pdb=" O HIS N 90 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS N 95 " --> pdb=" O LYS N 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 22 removed outlier: 3.578A pdb=" N VAL O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 84 removed outlier: 3.598A pdb=" N VAL O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY O 84 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 89 through 100 removed outlier: 4.249A pdb=" N LYS P 95 " --> pdb=" O LYS P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 89 through 100 removed outlier: 3.628A pdb=" N ALA Q 94 " --> pdb=" O HIS Q 90 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS Q 95 " --> pdb=" O LYS Q 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 36 through 38 current: chain 'G' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 82 current: chain 'G' and resid 114 through 129 removed outlier: 5.615A pdb=" N VAL G 123 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP G 143 " --> pdb=" O VAL G 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 137 through 144 current: chain 'B' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 38 current: chain 'B' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 82 current: chain 'B' and resid 114 through 129 removed outlier: 5.610A pdb=" N VAL B 123 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP B 143 " --> pdb=" O VAL B 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 144 current: chain 'E' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 38 current: chain 'E' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 82 current: chain 'E' and resid 114 through 129 removed outlier: 5.552A pdb=" N VAL E 123 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP E 143 " --> pdb=" O VAL E 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 137 through 144 current: chain 'J' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 36 through 38 current: chain 'J' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 68 through 82 current: chain 'J' and resid 114 through 129 removed outlier: 5.686A pdb=" N VAL J 123 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP J 143 " --> pdb=" O VAL J 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 137 through 144 current: chain 'M' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 36 through 38 current: chain 'M' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 82 current: chain 'M' and resid 114 through 129 removed outlier: 5.599A pdb=" N VAL M 123 " --> pdb=" O ASP M 143 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP M 143 " --> pdb=" O VAL M 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 137 through 144 current: chain 'P' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 36 through 38 current: chain 'P' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 68 through 82 current: chain 'P' and resid 114 through 129 removed outlier: 5.633A pdb=" N VAL P 123 " --> pdb=" O ASP P 143 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP P 143 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 36 through 38 current: chain 'g' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 68 through 82 current: chain 'g' and resid 114 through 129 removed outlier: 4.409A pdb=" N PHE g 117 " --> pdb=" O VAL g 149 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL g 149 " --> pdb=" O PHE g 117 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY g 119 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA g 147 " --> pdb=" O GLY g 119 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA g 121 " --> pdb=" O MET g 145 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N MET g 145 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL g 123 " --> pdb=" O ASP g 143 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP g 143 " --> pdb=" O VAL g 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 137 through 150 current: chain 'C' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 38 current: chain 'C' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 82 current: chain 'C' and resid 114 through 129 removed outlier: 5.592A pdb=" N VAL C 123 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 143 " --> pdb=" O VAL C 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 137 through 144 current: chain 'H' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 36 through 38 current: chain 'H' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 82 current: chain 'H' and resid 114 through 129 removed outlier: 5.560A pdb=" N VAL H 123 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP H 143 " --> pdb=" O VAL H 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 144 current: chain 'K' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 36 through 38 current: chain 'K' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 68 through 82 current: chain 'K' and resid 114 through 129 removed outlier: 5.647A pdb=" N VAL K 123 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP K 143 " --> pdb=" O VAL K 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 137 through 144 current: chain 'N' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 36 through 38 current: chain 'N' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 68 through 82 current: chain 'N' and resid 114 through 129 removed outlier: 4.616A pdb=" N PHE N 117 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL N 149 " --> pdb=" O PHE N 117 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY N 119 " --> pdb=" O ALA N 147 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA N 147 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA N 121 " --> pdb=" O MET N 145 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N MET N 145 " --> pdb=" O ALA N 121 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL N 123 " --> pdb=" O ASP N 143 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP N 143 " --> pdb=" O VAL N 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 137 through 150 current: chain 'Q' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 36 through 38 current: chain 'Q' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 68 through 82 current: chain 'Q' and resid 114 through 130 removed outlier: 5.590A pdb=" N VAL Q 123 " --> pdb=" O ASP Q 143 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP Q 143 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 25 through 26 removed outlier: 6.705A pdb=" N SER F 26 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N MET F 42 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG F 59 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN F 45 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS F 57 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU F 47 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS F 55 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F 124 " --> pdb=" O TRP F 54 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU F 56 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N CYS F 122 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR F 58 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER F 120 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE F 60 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 118 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE F 62 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER F 116 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N HIS F 64 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS F 114 " --> pdb=" O HIS F 64 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR F 66 " --> pdb=" O HIS F 112 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS F 112 " --> pdb=" O THR F 66 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 116 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS F 101 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU F 118 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS F 99 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N SER F 120 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG F 97 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS F 122 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N ALA F 95 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 11.837A pdb=" N GLU F 124 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N LEU F 93 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 46 removed outlier: 6.762A pdb=" N ARG A 59 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A 45 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 57 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 124 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A 56 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N CYS A 122 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR A 58 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER A 120 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 60 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 118 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 62 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER A 116 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS A 64 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A 114 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 66 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N HIS A 112 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 110 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 105 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS A 112 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN A 103 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 114 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 101 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 116 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 95 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS A 122 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 93 " --> pdb=" O CYS A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 47 removed outlier: 6.776A pdb=" N ARG D 59 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN D 45 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS D 57 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLU D 47 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS D 55 " --> pdb=" O GLU D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 66 current: chain 'D' and resid 110 through 125 Processing sheet with id=AA6, first strand: chain 'I' and resid 37 through 47 removed outlier: 6.864A pdb=" N ARG I 59 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN I 45 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS I 57 " --> pdb=" O GLN I 45 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU I 47 " --> pdb=" O LYS I 55 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS I 55 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU I 124 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU I 56 " --> pdb=" O CYS I 122 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N CYS I 122 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR I 58 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER I 120 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE I 60 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU I 118 " --> pdb=" O PHE I 60 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE I 62 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER I 116 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N HIS I 64 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS I 114 " --> pdb=" O HIS I 64 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR I 66 " --> pdb=" O HIS I 112 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N HIS I 112 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU I 110 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL I 105 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS I 112 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN I 103 " --> pdb=" O HIS I 112 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS I 114 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS I 101 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER I 116 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS I 99 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA I 95 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS I 122 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU I 93 " --> pdb=" O CYS I 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 37 through 47 removed outlier: 6.908A pdb=" N ARG L 59 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN L 45 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS L 57 " --> pdb=" O GLN L 45 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU L 47 " --> pdb=" O LYS L 55 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS L 55 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU L 124 " --> pdb=" O TRP L 54 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU L 56 " --> pdb=" O CYS L 122 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS L 122 " --> pdb=" O GLU L 56 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR L 58 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER L 120 " --> pdb=" O TYR L 58 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE L 60 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU L 118 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE L 62 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER L 116 " --> pdb=" O ILE L 62 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS L 64 " --> pdb=" O LYS L 114 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS L 114 " --> pdb=" O HIS L 64 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR L 66 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS L 112 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER L 116 " --> pdb=" O LYS L 101 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS L 101 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU L 118 " --> pdb=" O CYS L 99 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS L 99 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N SER L 120 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG L 97 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS L 122 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ALA L 95 " --> pdb=" O CYS L 122 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N GLU L 124 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N LEU L 93 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 25 through 26 removed outlier: 6.764A pdb=" N SER O 26 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N MET O 42 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG O 59 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN O 45 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS O 57 " --> pdb=" O GLN O 45 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU O 47 " --> pdb=" O LYS O 55 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS O 55 " --> pdb=" O GLU O 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 53 through 66 current: chain 'O' and resid 110 through 125 363 hydrogen bonds defined for protein. 1026 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: 2.85 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6522 1.34 - 1.46: 4396 1.46 - 1.58: 9103 1.58 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 20244 Sorted by residual: bond pdb=" CA MET C 145 " pdb=" CB MET C 145 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.33e-02 5.65e+03 1.73e+01 bond pdb=" CB PRO E 13 " pdb=" CG PRO E 13 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" CA LYS B 22 " pdb=" C LYS B 22 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.38e-02 5.25e+03 4.51e+00 bond pdb=" CA LYS M 22 " pdb=" C LYS M 22 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.35e+00 bond pdb=" CB LYS N 59 " pdb=" CG LYS N 59 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.93e+00 ... (remaining 20239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 26913 2.80 - 5.60: 290 5.60 - 8.40: 39 8.40 - 11.20: 12 11.20 - 14.01: 4 Bond angle restraints: 27258 Sorted by residual: angle pdb=" CA PRO E 13 " pdb=" N PRO E 13 " pdb=" CD PRO E 13 " ideal model delta sigma weight residual 112.00 98.27 13.73 1.40e+00 5.10e-01 9.62e+01 angle pdb=" CB LYS N 59 " pdb=" CG LYS N 59 " pdb=" CD LYS N 59 " ideal model delta sigma weight residual 111.30 123.09 -11.79 2.30e+00 1.89e-01 2.63e+01 angle pdb=" CB MET O 83 " pdb=" CG MET O 83 " pdb=" SD MET O 83 " ideal model delta sigma weight residual 112.70 126.71 -14.01 3.00e+00 1.11e-01 2.18e+01 angle pdb=" CA GLU H 134 " pdb=" CB GLU H 134 " pdb=" CG GLU H 134 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CA LYS N 59 " pdb=" CB LYS N 59 " pdb=" CG LYS N 59 " ideal model delta sigma weight residual 114.10 122.13 -8.03 2.00e+00 2.50e-01 1.61e+01 ... (remaining 27253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10577 17.93 - 35.85: 1250 35.85 - 53.78: 291 53.78 - 71.70: 72 71.70 - 89.63: 44 Dihedral angle restraints: 12234 sinusoidal: 4794 harmonic: 7440 Sorted by residual: dihedral pdb=" CA MET g 160 " pdb=" C MET g 160 " pdb=" N PRO g 161 " pdb=" CA PRO g 161 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU O 34 " pdb=" C GLU O 34 " pdb=" N MET O 35 " pdb=" CA MET O 35 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LYS Q 59 " pdb=" C LYS Q 59 " pdb=" N ASP Q 60 " pdb=" CA ASP Q 60 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 12231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2763 0.080 - 0.160: 319 0.160 - 0.240: 7 0.240 - 0.320: 0 0.320 - 0.400: 1 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CG LEU D 71 " pdb=" CB LEU D 71 " pdb=" CD1 LEU D 71 " pdb=" CD2 LEU D 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA MET F 1 " pdb=" N MET F 1 " pdb=" C MET F 1 " pdb=" CB MET F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CB ILE g 56 " pdb=" CA ILE g 56 " pdb=" CG1 ILE g 56 " pdb=" CG2 ILE g 56 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3087 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 12 " -0.113 5.00e-02 4.00e+02 1.58e-01 3.99e+01 pdb=" N PRO E 13 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET g 160 " 0.042 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO g 161 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO g 161 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO g 161 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 59 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LYS N 59 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS N 59 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP N 60 " -0.014 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 318 2.63 - 3.19: 17894 3.19 - 3.76: 31382 3.76 - 4.33: 43143 4.33 - 4.90: 71496 Nonbonded interactions: 164233 Sorted by model distance: nonbonded pdb=" OG1 THR D 66 " pdb=" O GLU D 68 " model vdw 2.057 3.040 nonbonded pdb=" OG SER P 58 " pdb=" OD1 ASP P 60 " model vdw 2.065 3.040 nonbonded pdb=" OG SER G 58 " pdb=" OD1 ASP G 60 " model vdw 2.093 3.040 nonbonded pdb=" OG SER N 58 " pdb=" OD1 ASP N 60 " model vdw 2.142 3.040 nonbonded pdb=" OG SER E 58 " pdb=" OD1 ASP E 60 " model vdw 2.158 3.040 ... (remaining 164228 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 'D' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 15 through 161) selection = chain 'C' selection = (chain 'E' and resid 15 through 161) selection = (chain 'G' and resid 15 through 161) selection = chain 'H' selection = (chain 'J' and resid 15 through 161) selection = chain 'K' selection = (chain 'M' and resid 15 through 161) selection = chain 'N' selection = (chain 'P' and resid 15 through 161) selection = chain 'Q' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.880 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 20250 Z= 0.196 Angle : 0.826 14.006 27270 Z= 0.461 Chirality : 0.048 0.400 3090 Planarity : 0.004 0.158 3486 Dihedral : 17.337 89.628 7452 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.59 % Favored : 93.14 % Rotamer: Outliers : 0.33 % Allowed : 27.54 % Favored : 72.13 % 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: -1.07 (0.16), residues: 2580 helix: 0.78 (0.29), residues: 336 sheet: 0.22 (0.16), residues: 1020 loop : -2.03 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 14 TYR 0.013 0.001 TYR E 83 PHE 0.018 0.002 PHE K 128 TRP 0.010 0.001 TRP B 75 HIS 0.005 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00406 (20244) covalent geometry : angle 0.82575 (27258) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.40958 ( 12) hydrogen bonds : bond 0.20678 ( 363) hydrogen bonds : angle 7.95703 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.8791 (tpp) cc_final: 0.7853 (tpp) REVERT: B 145 MET cc_start: 0.9024 (ptm) cc_final: 0.8771 (mtm) REVERT: C 145 MET cc_start: 0.8929 (ptp) cc_final: 0.8698 (pmm) REVERT: E 145 MET cc_start: 0.9276 (ptp) cc_final: 0.8470 (pmm) REVERT: K 55 GLU cc_start: 0.9093 (tt0) cc_final: 0.8697 (tp30) REVERT: K 150 ASP cc_start: 0.8773 (m-30) cc_final: 0.8402 (t0) REVERT: L 39 MET cc_start: 0.8877 (mtp) cc_final: 0.8331 (mtp) REVERT: M 109 ASN cc_start: 0.9372 (t0) cc_final: 0.9115 (t0) REVERT: O 24 ASP cc_start: 0.8751 (m-30) cc_final: 0.8462 (p0) REVERT: O 103 ASN cc_start: 0.8437 (t0) cc_final: 0.8056 (m-40) REVERT: P 72 MET cc_start: 0.8720 (tpp) cc_final: 0.8435 (tpp) outliers start: 7 outliers final: 4 residues processed: 246 average time/residue: 0.1328 time to fit residues: 53.2776 Evaluate side-chains 232 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.047898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038736 restraints weight = 100060.885| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.83 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20250 Z= 0.286 Angle : 0.695 8.711 27270 Z= 0.354 Chirality : 0.046 0.168 3090 Planarity : 0.004 0.065 3486 Dihedral : 5.183 36.772 2732 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.02 % Favored : 92.71 % Rotamer: Outliers : 3.77 % Allowed : 22.69 % Favored : 73.54 % 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: -0.94 (0.16), residues: 2580 helix: 1.14 (0.29), residues: 330 sheet: 0.03 (0.15), residues: 1056 loop : -1.77 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 14 TYR 0.016 0.002 TYR G 96 PHE 0.011 0.002 PHE M 132 TRP 0.011 0.001 TRP K 65 HIS 0.007 0.001 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00627 (20244) covalent geometry : angle 0.69511 (27258) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.35398 ( 12) hydrogen bonds : bond 0.04223 ( 363) hydrogen bonds : angle 5.47673 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 224 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 145 MET cc_start: 0.8719 (ptm) cc_final: 0.8452 (ptp) REVERT: g 72 MET cc_start: 0.9137 (mmm) cc_final: 0.8599 (mmm) REVERT: g 88 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8853 (tm-30) REVERT: g 143 ASP cc_start: 0.8337 (t0) cc_final: 0.7979 (t0) REVERT: A 16 MET cc_start: 0.8356 (tmm) cc_final: 0.7941 (tmt) REVERT: A 42 MET cc_start: 0.7018 (mmm) cc_final: 0.6545 (mmm) REVERT: B 72 MET cc_start: 0.9073 (tpp) cc_final: 0.8774 (tpt) REVERT: B 143 ASP cc_start: 0.8577 (p0) cc_final: 0.8353 (t0) REVERT: C 128 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6961 (p90) REVERT: C 129 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 145 MET cc_start: 0.8759 (ptp) cc_final: 0.8356 (pmm) REVERT: D 29 MET cc_start: 0.8435 (mmm) cc_final: 0.7969 (tpp) REVERT: E 145 MET cc_start: 0.9158 (ptp) cc_final: 0.8570 (pmm) REVERT: H 72 MET cc_start: 0.8241 (mmm) cc_final: 0.7760 (mmm) REVERT: H 74 GLU cc_start: 0.8725 (pm20) cc_final: 0.8119 (pm20) REVERT: H 134 GLU cc_start: 0.8118 (tp30) cc_final: 0.7891 (tp30) REVERT: J 3 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: J 60 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8353 (p0) REVERT: J 72 MET cc_start: 0.8613 (mmm) cc_final: 0.8266 (mmm) REVERT: J 150 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8865 (t0) REVERT: K 55 GLU cc_start: 0.9082 (tt0) cc_final: 0.8735 (tp30) REVERT: K 78 GLU cc_start: 0.8589 (mp0) cc_final: 0.8388 (mp0) REVERT: K 88 GLU cc_start: 0.8420 (tp30) cc_final: 0.8173 (tp30) REVERT: K 92 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8829 (mm-30) REVERT: K 150 ASP cc_start: 0.8758 (m-30) cc_final: 0.8198 (t0) REVERT: M 72 MET cc_start: 0.9359 (mmm) cc_final: 0.8740 (mmm) REVERT: M 76 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9328 (t) REVERT: N 72 MET cc_start: 0.8387 (mmm) cc_final: 0.8112 (mmm) REVERT: N 74 GLU cc_start: 0.8820 (pm20) cc_final: 0.8416 (pm20) REVERT: N 128 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7976 (p90) REVERT: O 24 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8517 (p0) REVERT: O 116 SER cc_start: 0.8621 (t) cc_final: 0.8373 (p) REVERT: P 11 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: P 160 MET cc_start: 0.8825 (tpp) cc_final: 0.8517 (tpp) outliers start: 80 outliers final: 39 residues processed: 279 average time/residue: 0.1317 time to fit residues: 60.5168 Evaluate side-chains 260 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 24 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 128 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN Q 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.046523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037445 restraints weight = 101418.299| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 4.78 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 20250 Z= 0.319 Angle : 0.723 12.919 27270 Z= 0.362 Chirality : 0.046 0.199 3090 Planarity : 0.004 0.061 3486 Dihedral : 5.177 29.397 2724 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.29 % Favored : 92.44 % Rotamer: Outliers : 5.13 % Allowed : 22.46 % Favored : 72.41 % 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: -0.99 (0.16), residues: 2580 helix: 1.21 (0.29), residues: 330 sheet: -0.10 (0.15), residues: 1062 loop : -1.73 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 8 TYR 0.016 0.002 TYR K 126 PHE 0.011 0.002 PHE I 6 TRP 0.012 0.002 TRP K 65 HIS 0.007 0.001 HIS L 63 Details of bonding type rmsd covalent geometry : bond 0.00697 (20244) covalent geometry : angle 0.72305 (27258) SS BOND : bond 0.00437 ( 6) SS BOND : angle 0.43436 ( 12) hydrogen bonds : bond 0.03954 ( 363) hydrogen bonds : angle 5.28179 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 228 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 74 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: g 72 MET cc_start: 0.9197 (mmm) cc_final: 0.8574 (mmm) REVERT: g 143 ASP cc_start: 0.8475 (t0) cc_final: 0.7992 (t0) REVERT: A 16 MET cc_start: 0.8465 (tmm) cc_final: 0.7902 (tmt) REVERT: A 42 MET cc_start: 0.7510 (mmm) cc_final: 0.7028 (mmm) REVERT: A 69 GLN cc_start: 0.8553 (tp-100) cc_final: 0.7923 (mt0) REVERT: B 72 MET cc_start: 0.9114 (tpp) cc_final: 0.8534 (tpt) REVERT: C 128 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7111 (p90) REVERT: C 129 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7815 (mm-30) REVERT: C 134 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: C 145 MET cc_start: 0.8689 (ptp) cc_final: 0.8329 (pmm) REVERT: D 7 MET cc_start: 0.9130 (tpp) cc_final: 0.8828 (tmm) REVERT: D 29 MET cc_start: 0.8607 (mmm) cc_final: 0.8139 (tpp) REVERT: H 66 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8203 (mttp) REVERT: H 72 MET cc_start: 0.8378 (mmm) cc_final: 0.7847 (mmm) REVERT: H 74 GLU cc_start: 0.8872 (pm20) cc_final: 0.7992 (pm20) REVERT: I 7 MET cc_start: 0.8972 (tpt) cc_final: 0.8637 (tpp) REVERT: I 83 MET cc_start: 0.8917 (tmm) cc_final: 0.8692 (tmm) REVERT: I 110 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8672 (pp) REVERT: J 3 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8682 (m-10) REVERT: J 51 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8710 (tttp) REVERT: J 60 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8323 (p0) REVERT: J 72 MET cc_start: 0.8792 (mmm) cc_final: 0.8122 (mmm) REVERT: K 55 GLU cc_start: 0.9125 (tt0) cc_final: 0.8847 (tp30) REVERT: K 78 GLU cc_start: 0.8796 (mp0) cc_final: 0.8388 (mp0) REVERT: K 88 GLU cc_start: 0.8640 (tp30) cc_final: 0.8386 (tp30) REVERT: K 92 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8885 (mm-30) REVERT: K 128 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8035 (p90) REVERT: K 150 ASP cc_start: 0.8754 (m-30) cc_final: 0.8201 (t0) REVERT: M 72 MET cc_start: 0.9539 (mmm) cc_final: 0.8763 (mmm) REVERT: M 76 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9241 (t) REVERT: N 72 MET cc_start: 0.8281 (mmm) cc_final: 0.8053 (mmm) REVERT: N 74 GLU cc_start: 0.8859 (pm20) cc_final: 0.8333 (pm20) REVERT: N 128 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7963 (p90) REVERT: N 129 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: O 24 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8581 (p0) REVERT: P 11 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: P 145 MET cc_start: 0.8852 (ttm) cc_final: 0.8517 (mtp) outliers start: 109 outliers final: 55 residues processed: 314 average time/residue: 0.1272 time to fit residues: 65.0673 Evaluate side-chains 282 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 ASP Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 99 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 ASN N 90 HIS O 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038502 restraints weight = 99780.200| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.76 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20250 Z= 0.180 Angle : 0.626 10.186 27270 Z= 0.314 Chirality : 0.045 0.181 3090 Planarity : 0.003 0.060 3486 Dihedral : 4.841 29.077 2724 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 3.48 % Allowed : 25.33 % Favored : 71.19 % 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: -0.82 (0.16), residues: 2580 helix: 1.58 (0.30), residues: 330 sheet: -0.08 (0.16), residues: 1062 loop : -1.60 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 97 TYR 0.011 0.001 TYR A 58 PHE 0.010 0.001 PHE F 6 TRP 0.009 0.001 TRP P 75 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00400 (20244) covalent geometry : angle 0.62590 (27258) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.38118 ( 12) hydrogen bonds : bond 0.03193 ( 363) hydrogen bonds : angle 5.05470 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 234 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 136 MET cc_start: 0.9221 (ppp) cc_final: 0.8751 (ppp) REVERT: g 55 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8402 (tm-30) REVERT: g 72 MET cc_start: 0.9040 (mmm) cc_final: 0.8613 (mmm) REVERT: g 143 ASP cc_start: 0.8493 (t0) cc_final: 0.7936 (t0) REVERT: A 16 MET cc_start: 0.8497 (tmm) cc_final: 0.8055 (tmm) REVERT: A 42 MET cc_start: 0.7270 (mmm) cc_final: 0.6923 (mmm) REVERT: B 72 MET cc_start: 0.9053 (tpp) cc_final: 0.8502 (tpt) REVERT: B 143 ASP cc_start: 0.8678 (p0) cc_final: 0.8334 (t70) REVERT: C 128 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7045 (p90) REVERT: C 129 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7887 (mm-30) REVERT: C 134 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: D 7 MET cc_start: 0.9128 (tpp) cc_final: 0.8800 (tmm) REVERT: D 29 MET cc_start: 0.8575 (mmm) cc_final: 0.8085 (tpp) REVERT: D 83 MET cc_start: 0.7915 (mmp) cc_final: 0.7674 (mmp) REVERT: E 60 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (p0) REVERT: E 72 MET cc_start: 0.8984 (mmm) cc_final: 0.8691 (mmm) REVERT: E 145 MET cc_start: 0.9181 (ptp) cc_final: 0.8445 (pmm) REVERT: H 72 MET cc_start: 0.8337 (mmm) cc_final: 0.7810 (mmm) REVERT: H 74 GLU cc_start: 0.8861 (pm20) cc_final: 0.7743 (pm20) REVERT: H 129 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7439 (tm-30) REVERT: I 7 MET cc_start: 0.8993 (tpt) cc_final: 0.8781 (tpp) REVERT: I 83 MET cc_start: 0.8890 (tmm) cc_final: 0.8689 (tmm) REVERT: I 110 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (pp) REVERT: J 3 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: J 51 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8839 (tttm) REVERT: J 60 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8034 (p0) REVERT: J 72 MET cc_start: 0.8787 (mmm) cc_final: 0.8025 (mmm) REVERT: J 150 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8889 (t0) REVERT: K 55 GLU cc_start: 0.9106 (tt0) cc_final: 0.8846 (tp30) REVERT: K 78 GLU cc_start: 0.8744 (mp0) cc_final: 0.8282 (mp0) REVERT: K 88 GLU cc_start: 0.8483 (tp30) cc_final: 0.8168 (tp30) REVERT: K 92 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8872 (mm-30) REVERT: K 128 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7925 (p90) REVERT: L 29 MET cc_start: 0.8308 (tpp) cc_final: 0.8059 (tpp) REVERT: M 3 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: M 72 MET cc_start: 0.9568 (mmm) cc_final: 0.8783 (mmm) REVERT: N 72 MET cc_start: 0.8258 (mmm) cc_final: 0.8040 (mmm) REVERT: N 74 GLU cc_start: 0.8810 (pm20) cc_final: 0.8274 (pm20) REVERT: N 128 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7922 (p90) REVERT: N 129 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: O 24 ASP cc_start: 0.8824 (m-30) cc_final: 0.8539 (p0) REVERT: P 11 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7880 (m-80) outliers start: 74 outliers final: 39 residues processed: 283 average time/residue: 0.1251 time to fit residues: 58.4431 Evaluate side-chains 272 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 128 PHE Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.037553 restraints weight = 101288.174| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.76 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20250 Z= 0.255 Angle : 0.680 11.093 27270 Z= 0.336 Chirality : 0.045 0.185 3090 Planarity : 0.003 0.060 3486 Dihedral : 4.876 28.540 2724 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.44 % Favored : 92.25 % Rotamer: Outliers : 4.43 % Allowed : 25.38 % Favored : 70.20 % 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: -0.83 (0.16), residues: 2580 helix: 1.59 (0.29), residues: 336 sheet: -0.11 (0.16), residues: 1062 loop : -1.60 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 8 TYR 0.012 0.001 TYR K 126 PHE 0.013 0.001 PHE N 29 TRP 0.010 0.001 TRP P 75 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00560 (20244) covalent geometry : angle 0.68018 (27258) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.40925 ( 12) hydrogen bonds : bond 0.03326 ( 363) hydrogen bonds : angle 5.05174 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 228 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 74 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8624 (pp20) REVERT: G 77 ILE cc_start: 0.9593 (mm) cc_final: 0.9377 (mm) REVERT: g 55 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8295 (tm-30) REVERT: g 72 MET cc_start: 0.8891 (mmm) cc_final: 0.8446 (mmm) REVERT: g 143 ASP cc_start: 0.8584 (t0) cc_final: 0.8119 (t0) REVERT: A 16 MET cc_start: 0.8396 (tmm) cc_final: 0.8103 (tmt) REVERT: A 42 MET cc_start: 0.7394 (mmm) cc_final: 0.7109 (mmm) REVERT: A 58 TYR cc_start: 0.6827 (m-80) cc_final: 0.6590 (m-80) REVERT: A 69 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7944 (mt0) REVERT: B 72 MET cc_start: 0.9039 (tpp) cc_final: 0.8542 (tpt) REVERT: C 128 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7024 (p90) REVERT: C 129 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 134 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: D 29 MET cc_start: 0.8647 (mmm) cc_final: 0.8152 (tpp) REVERT: D 83 MET cc_start: 0.7925 (mmp) cc_final: 0.7718 (mmm) REVERT: E 60 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8056 (p0) REVERT: H 72 MET cc_start: 0.8293 (mmm) cc_final: 0.7746 (mmm) REVERT: H 74 GLU cc_start: 0.8974 (pm20) cc_final: 0.7774 (pm20) REVERT: H 129 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7585 (tm-30) REVERT: I 83 MET cc_start: 0.8926 (tmm) cc_final: 0.8708 (tmm) REVERT: J 3 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: J 51 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8763 (tttp) REVERT: J 60 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8259 (p0) REVERT: J 72 MET cc_start: 0.8877 (mmm) cc_final: 0.8073 (mmm) REVERT: J 150 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8885 (t0) REVERT: K 55 GLU cc_start: 0.9091 (tt0) cc_final: 0.8697 (tp30) REVERT: K 59 LYS cc_start: 0.8004 (tppt) cc_final: 0.7775 (tptm) REVERT: K 72 MET cc_start: 0.8150 (tpt) cc_final: 0.7675 (tmm) REVERT: K 78 GLU cc_start: 0.8775 (mp0) cc_final: 0.8277 (mp0) REVERT: K 88 GLU cc_start: 0.8517 (tp30) cc_final: 0.8285 (tp30) REVERT: K 128 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.7976 (p90) REVERT: L 29 MET cc_start: 0.8358 (tpp) cc_final: 0.7892 (tpp) REVERT: L 39 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7640 (mtp) REVERT: L 107 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: M 72 MET cc_start: 0.9598 (mmm) cc_final: 0.8674 (mmm) REVERT: M 136 MET cc_start: 0.9074 (ppp) cc_final: 0.8795 (ppp) REVERT: N 72 MET cc_start: 0.8229 (mmm) cc_final: 0.8013 (mmm) REVERT: N 74 GLU cc_start: 0.8787 (pm20) cc_final: 0.8275 (pm20) REVERT: N 128 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7955 (p90) REVERT: N 129 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: O 24 ASP cc_start: 0.8835 (m-30) cc_final: 0.8577 (p0) REVERT: P 11 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: P 72 MET cc_start: 0.9224 (tpp) cc_final: 0.8878 (tpp) outliers start: 94 outliers final: 52 residues processed: 302 average time/residue: 0.1317 time to fit residues: 65.4778 Evaluate side-chains 279 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 39 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 196 optimal weight: 0.0970 chunk 193 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 HIS ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.046858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037769 restraints weight = 100550.685| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.75 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20250 Z= 0.213 Angle : 0.651 12.577 27270 Z= 0.322 Chirality : 0.045 0.171 3090 Planarity : 0.003 0.065 3486 Dihedral : 4.773 29.871 2724 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.94 % Favored : 92.75 % Rotamer: Outliers : 4.24 % Allowed : 25.66 % Favored : 70.10 % 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: -0.77 (0.16), residues: 2580 helix: 1.86 (0.29), residues: 336 sheet: -0.10 (0.16), residues: 1050 loop : -1.59 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 14 TYR 0.010 0.001 TYR K 126 PHE 0.017 0.001 PHE I 6 TRP 0.008 0.001 TRP I 54 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00470 (20244) covalent geometry : angle 0.65075 (27258) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.39183 ( 12) hydrogen bonds : bond 0.03092 ( 363) hydrogen bonds : angle 4.98055 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 228 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9585 (mm) cc_final: 0.9377 (mm) REVERT: G 136 MET cc_start: 0.9204 (ppp) cc_final: 0.8738 (ppp) REVERT: g 55 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8385 (tm-30) REVERT: g 72 MET cc_start: 0.9126 (mmm) cc_final: 0.8573 (mmm) REVERT: g 143 ASP cc_start: 0.8593 (t0) cc_final: 0.8103 (t0) REVERT: A 16 MET cc_start: 0.8444 (tmm) cc_final: 0.8128 (tmt) REVERT: A 42 MET cc_start: 0.7235 (mmm) cc_final: 0.6885 (mmm) REVERT: A 58 TYR cc_start: 0.6938 (m-80) cc_final: 0.6688 (m-80) REVERT: A 69 GLN cc_start: 0.8561 (tp-100) cc_final: 0.7868 (mt0) REVERT: B 67 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.9034 (p) REVERT: B 72 MET cc_start: 0.9028 (tpp) cc_final: 0.8513 (tpt) REVERT: C 128 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.6987 (p90) REVERT: C 129 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7876 (mm-30) REVERT: C 134 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 7 MET cc_start: 0.9125 (tpp) cc_final: 0.8758 (tmm) REVERT: D 29 MET cc_start: 0.8651 (mmm) cc_final: 0.8194 (tpp) REVERT: D 83 MET cc_start: 0.8023 (mmp) cc_final: 0.7822 (mmm) REVERT: E 60 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (p0) REVERT: E 145 MET cc_start: 0.9167 (ptp) cc_final: 0.8463 (pmm) REVERT: H 72 MET cc_start: 0.8362 (mmm) cc_final: 0.7841 (mmm) REVERT: H 74 GLU cc_start: 0.9008 (pm20) cc_final: 0.7812 (pm20) REVERT: H 88 GLU cc_start: 0.8919 (tp30) cc_final: 0.8630 (tp30) REVERT: I 83 MET cc_start: 0.8917 (tmm) cc_final: 0.8676 (tmm) REVERT: J 3 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: J 51 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8852 (tttm) REVERT: J 60 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8244 (p0) REVERT: J 72 MET cc_start: 0.8925 (mmm) cc_final: 0.8155 (mmm) REVERT: J 150 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8890 (t0) REVERT: K 72 MET cc_start: 0.8256 (tpt) cc_final: 0.7950 (mmm) REVERT: K 78 GLU cc_start: 0.8780 (mp0) cc_final: 0.8255 (mp0) REVERT: K 128 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.7962 (p90) REVERT: L 29 MET cc_start: 0.8450 (tpp) cc_final: 0.7987 (tpp) REVERT: L 39 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7690 (mtp) REVERT: M 3 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: M 72 MET cc_start: 0.9576 (mmm) cc_final: 0.8614 (mmm) REVERT: M 136 MET cc_start: 0.9032 (ppp) cc_final: 0.8743 (ppp) REVERT: N 66 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8682 (ttmm) REVERT: N 72 MET cc_start: 0.8327 (mmm) cc_final: 0.8078 (mmm) REVERT: N 74 GLU cc_start: 0.8757 (pm20) cc_final: 0.8144 (pm20) REVERT: N 128 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7993 (p90) REVERT: N 129 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: O 24 ASP cc_start: 0.8825 (m-30) cc_final: 0.8541 (p0) REVERT: P 11 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: P 145 MET cc_start: 0.8906 (ttm) cc_final: 0.8547 (mtp) outliers start: 90 outliers final: 54 residues processed: 298 average time/residue: 0.1274 time to fit residues: 62.6733 Evaluate side-chains 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 39 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 176 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.046719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037666 restraints weight = 100677.990| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 4.73 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20250 Z= 0.214 Angle : 0.669 13.328 27270 Z= 0.328 Chirality : 0.045 0.180 3090 Planarity : 0.003 0.067 3486 Dihedral : 4.695 29.257 2724 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.13 % Favored : 92.56 % Rotamer: Outliers : 4.38 % Allowed : 26.18 % Favored : 69.44 % 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: -0.79 (0.16), residues: 2580 helix: 1.90 (0.29), residues: 336 sheet: -0.15 (0.16), residues: 1050 loop : -1.59 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 14 TYR 0.010 0.001 TYR J 83 PHE 0.018 0.001 PHE I 6 TRP 0.008 0.001 TRP K 65 HIS 0.008 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00476 (20244) covalent geometry : angle 0.66927 (27258) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.39115 ( 12) hydrogen bonds : bond 0.03074 ( 363) hydrogen bonds : angle 4.95333 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 220 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9583 (mm) cc_final: 0.9380 (mm) REVERT: G 136 MET cc_start: 0.9211 (ppp) cc_final: 0.8963 (ppp) REVERT: g 55 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8415 (tm-30) REVERT: g 72 MET cc_start: 0.9173 (mmm) cc_final: 0.8590 (mmm) REVERT: g 143 ASP cc_start: 0.8603 (t0) cc_final: 0.8169 (t0) REVERT: A 16 MET cc_start: 0.8426 (tmm) cc_final: 0.8090 (tmt) REVERT: A 42 MET cc_start: 0.7247 (mmm) cc_final: 0.6826 (mmm) REVERT: B 67 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8977 (p) REVERT: B 72 MET cc_start: 0.9037 (tpp) cc_final: 0.8523 (tpt) REVERT: C 128 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6943 (p90) REVERT: C 129 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7876 (mm-30) REVERT: C 134 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 29 MET cc_start: 0.8685 (mmm) cc_final: 0.8228 (tpp) REVERT: D 83 MET cc_start: 0.8047 (mmp) cc_final: 0.7836 (mmm) REVERT: E 60 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (p0) REVERT: H 72 MET cc_start: 0.8423 (mmm) cc_final: 0.7974 (mmm) REVERT: H 74 GLU cc_start: 0.9015 (pm20) cc_final: 0.7815 (pm20) REVERT: H 88 GLU cc_start: 0.8908 (tp30) cc_final: 0.8596 (tp30) REVERT: H 134 GLU cc_start: 0.7851 (tp30) cc_final: 0.7650 (tp30) REVERT: I 83 MET cc_start: 0.8909 (tmm) cc_final: 0.8662 (tmm) REVERT: J 3 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: J 51 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8816 (tttm) REVERT: J 60 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8288 (p0) REVERT: J 150 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8885 (t0) REVERT: K 55 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8835 (tp30) REVERT: K 72 MET cc_start: 0.8244 (tpt) cc_final: 0.7965 (mmm) REVERT: K 78 GLU cc_start: 0.8766 (mp0) cc_final: 0.8229 (mp0) REVERT: K 92 GLU cc_start: 0.9217 (tp30) cc_final: 0.8997 (tp30) REVERT: K 128 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.7957 (p90) REVERT: L 29 MET cc_start: 0.8493 (tpp) cc_final: 0.8176 (tpp) REVERT: M 3 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: M 72 MET cc_start: 0.9598 (mmm) cc_final: 0.8625 (mmm) REVERT: M 136 MET cc_start: 0.9035 (ppp) cc_final: 0.8751 (ppp) REVERT: N 66 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8647 (ttmm) REVERT: N 72 MET cc_start: 0.8274 (mmm) cc_final: 0.8056 (mmm) REVERT: N 74 GLU cc_start: 0.8742 (pm20) cc_final: 0.8178 (pm20) REVERT: N 128 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7991 (p90) REVERT: N 129 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: O 24 ASP cc_start: 0.8823 (m-30) cc_final: 0.8557 (p0) REVERT: P 11 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: P 145 MET cc_start: 0.9063 (ttm) cc_final: 0.8680 (mtp) outliers start: 93 outliers final: 60 residues processed: 293 average time/residue: 0.1256 time to fit residues: 61.5362 Evaluate side-chains 291 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 129 GLU Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 HIS ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.046448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037436 restraints weight = 100715.845| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 4.71 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20250 Z= 0.225 Angle : 0.680 12.738 27270 Z= 0.334 Chirality : 0.045 0.174 3090 Planarity : 0.003 0.070 3486 Dihedral : 4.724 29.822 2724 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.21 % Favored : 92.44 % Rotamer: Outliers : 4.43 % Allowed : 26.32 % Favored : 69.26 % 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: -0.81 (0.17), residues: 2580 helix: 1.91 (0.29), residues: 336 sheet: -0.18 (0.16), residues: 1050 loop : -1.59 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 14 TYR 0.011 0.001 TYR J 83 PHE 0.018 0.001 PHE I 6 TRP 0.008 0.001 TRP K 65 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00500 (20244) covalent geometry : angle 0.68003 (27258) SS BOND : bond 0.00303 ( 6) SS BOND : angle 0.37815 ( 12) hydrogen bonds : bond 0.03072 ( 363) hydrogen bonds : angle 4.97884 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 220 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9577 (mm) cc_final: 0.9366 (mm) REVERT: G 136 MET cc_start: 0.9213 (ppp) cc_final: 0.8972 (ppp) REVERT: g 55 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8374 (tm-30) REVERT: g 72 MET cc_start: 0.9170 (mmm) cc_final: 0.8591 (mmm) REVERT: g 143 ASP cc_start: 0.8602 (t0) cc_final: 0.8169 (t0) REVERT: g 160 MET cc_start: 0.8857 (mmm) cc_final: 0.8596 (mmt) REVERT: A 16 MET cc_start: 0.8443 (tmm) cc_final: 0.8108 (tmt) REVERT: A 42 MET cc_start: 0.7288 (mmm) cc_final: 0.6859 (mmm) REVERT: A 58 TYR cc_start: 0.7036 (m-80) cc_final: 0.6717 (m-80) REVERT: A 69 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7865 (mt0) REVERT: B 67 SER cc_start: 0.9423 (OUTLIER) cc_final: 0.8961 (p) REVERT: B 72 MET cc_start: 0.9032 (tpp) cc_final: 0.8509 (tpt) REVERT: C 67 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8737 (p) REVERT: C 128 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6944 (p90) REVERT: C 129 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7798 (mm-30) REVERT: C 134 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 29 MET cc_start: 0.8683 (mmm) cc_final: 0.8237 (tpp) REVERT: E 60 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7696 (p0) REVERT: E 145 MET cc_start: 0.9212 (ptp) cc_final: 0.8548 (pmm) REVERT: H 72 MET cc_start: 0.8489 (mmm) cc_final: 0.7967 (mmm) REVERT: H 74 GLU cc_start: 0.9017 (pm20) cc_final: 0.7789 (pm20) REVERT: H 88 GLU cc_start: 0.8905 (tp30) cc_final: 0.8591 (tp30) REVERT: H 129 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7615 (tm-30) REVERT: I 83 MET cc_start: 0.8911 (tmm) cc_final: 0.8663 (tmm) REVERT: J 3 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: J 51 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8759 (ttmm) REVERT: J 60 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8299 (p0) REVERT: J 136 MET cc_start: 0.9327 (ttp) cc_final: 0.8781 (ppp) REVERT: J 150 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8848 (t0) REVERT: K 55 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8849 (tp30) REVERT: K 72 MET cc_start: 0.8262 (tpt) cc_final: 0.7616 (mmm) REVERT: K 78 GLU cc_start: 0.8770 (mp0) cc_final: 0.8230 (mp0) REVERT: K 92 GLU cc_start: 0.9215 (tp30) cc_final: 0.8983 (tp30) REVERT: K 128 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7960 (p90) REVERT: M 3 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: M 72 MET cc_start: 0.9607 (mmm) cc_final: 0.8679 (mmm) REVERT: M 136 MET cc_start: 0.9070 (ppp) cc_final: 0.8791 (ppp) REVERT: N 66 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8579 (ttmm) REVERT: N 67 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (p) REVERT: N 72 MET cc_start: 0.8339 (mmm) cc_final: 0.8095 (mmm) REVERT: N 74 GLU cc_start: 0.8755 (pm20) cc_final: 0.8208 (pm20) REVERT: N 128 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8009 (p90) REVERT: N 129 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: O 24 ASP cc_start: 0.8809 (m-30) cc_final: 0.8561 (p0) REVERT: P 11 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7736 (m-80) outliers start: 94 outliers final: 65 residues processed: 291 average time/residue: 0.1164 time to fit residues: 56.6639 Evaluate side-chains 295 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 213 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 129 GLU Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 110 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.046008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.037052 restraints weight = 100807.461| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.69 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20250 Z= 0.265 Angle : 0.728 14.633 27270 Z= 0.354 Chirality : 0.046 0.180 3090 Planarity : 0.003 0.072 3486 Dihedral : 4.812 25.635 2724 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.33 % Favored : 92.33 % Rotamer: Outliers : 4.33 % Allowed : 26.32 % Favored : 69.35 % 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: -0.90 (0.16), residues: 2580 helix: 1.83 (0.29), residues: 336 sheet: -0.30 (0.16), residues: 1044 loop : -1.58 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 14 TYR 0.016 0.001 TYR I 58 PHE 0.020 0.002 PHE I 6 TRP 0.011 0.001 TRP K 65 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00587 (20244) covalent geometry : angle 0.72833 (27258) SS BOND : bond 0.00391 ( 6) SS BOND : angle 0.40258 ( 12) hydrogen bonds : bond 0.03241 ( 363) hydrogen bonds : angle 5.05027 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 217 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9568 (mm) cc_final: 0.9359 (mm) REVERT: G 136 MET cc_start: 0.9234 (ppp) cc_final: 0.8990 (ppp) REVERT: g 55 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8381 (tm-30) REVERT: g 72 MET cc_start: 0.9168 (mmm) cc_final: 0.8500 (mmm) REVERT: g 143 ASP cc_start: 0.8698 (t0) cc_final: 0.8236 (t0) REVERT: F 7 MET cc_start: 0.9197 (tpt) cc_final: 0.8853 (tpt) REVERT: F 29 MET cc_start: 0.7988 (mmm) cc_final: 0.7636 (tpp) REVERT: A 16 MET cc_start: 0.8466 (tmm) cc_final: 0.8137 (tmt) REVERT: A 42 MET cc_start: 0.7367 (mmm) cc_final: 0.6899 (mmm) REVERT: A 69 GLN cc_start: 0.8493 (tp-100) cc_final: 0.7975 (mt0) REVERT: B 72 MET cc_start: 0.9032 (tpp) cc_final: 0.8757 (tpp) REVERT: C 67 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8212 (p) REVERT: C 128 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.6915 (p90) REVERT: C 129 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7874 (mm-30) REVERT: C 134 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: D 29 MET cc_start: 0.8696 (mmm) cc_final: 0.8268 (tpp) REVERT: E 60 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7762 (p0) REVERT: E 72 MET cc_start: 0.8842 (mmm) cc_final: 0.8081 (tpp) REVERT: H 72 MET cc_start: 0.8543 (mmm) cc_final: 0.7901 (mmm) REVERT: H 74 GLU cc_start: 0.9062 (pm20) cc_final: 0.8095 (pm20) REVERT: H 88 GLU cc_start: 0.8916 (tp30) cc_final: 0.8618 (tp30) REVERT: I 39 MET cc_start: 0.8952 (mtp) cc_final: 0.8735 (mtp) REVERT: I 83 MET cc_start: 0.8950 (tmm) cc_final: 0.8714 (tmm) REVERT: J 51 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8829 (ttmm) REVERT: J 60 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8457 (p0) REVERT: J 136 MET cc_start: 0.9369 (ttp) cc_final: 0.8520 (tmm) REVERT: K 55 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: K 72 MET cc_start: 0.8239 (tpt) cc_final: 0.7696 (mmm) REVERT: K 78 GLU cc_start: 0.8771 (mp0) cc_final: 0.8234 (mp0) REVERT: K 92 GLU cc_start: 0.9238 (tp30) cc_final: 0.9007 (tp30) REVERT: K 128 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.7985 (p90) REVERT: M 72 MET cc_start: 0.9600 (mmm) cc_final: 0.8707 (mmm) REVERT: M 136 MET cc_start: 0.9103 (ppp) cc_final: 0.8836 (ppp) REVERT: N 66 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8656 (ttmm) REVERT: N 67 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8207 (p) REVERT: N 72 MET cc_start: 0.8295 (mmm) cc_final: 0.8023 (mmm) REVERT: N 74 GLU cc_start: 0.8770 (pm20) cc_final: 0.8229 (pm20) REVERT: N 128 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8068 (p90) REVERT: N 129 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: O 24 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8593 (p0) REVERT: P 11 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7769 (m-80) outliers start: 92 outliers final: 64 residues processed: 288 average time/residue: 0.1145 time to fit residues: 55.2581 Evaluate side-chains 290 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 212 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 36 LEU Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 129 GLU Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 24 ASP Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 58 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 220 optimal weight: 0.3980 chunk 241 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.047804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038834 restraints weight = 99581.633| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 4.73 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20250 Z= 0.123 Angle : 0.654 14.021 27270 Z= 0.317 Chirality : 0.045 0.178 3090 Planarity : 0.003 0.069 3486 Dihedral : 4.403 23.717 2724 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.12 % Favored : 93.57 % Rotamer: Outliers : 2.82 % Allowed : 27.73 % Favored : 69.44 % 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: -0.80 (0.16), residues: 2580 helix: 2.20 (0.29), residues: 336 sheet: -0.35 (0.16), residues: 1008 loop : -1.45 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 14 TYR 0.007 0.001 TYR E 11 PHE 0.016 0.001 PHE I 6 TRP 0.010 0.001 TRP B 65 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00286 (20244) covalent geometry : angle 0.65366 (27258) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.35706 ( 12) hydrogen bonds : bond 0.02689 ( 363) hydrogen bonds : angle 4.88559 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9545 (mm) cc_final: 0.9339 (mm) REVERT: G 136 MET cc_start: 0.9197 (ppp) cc_final: 0.8977 (ppp) REVERT: g 55 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8280 (tm-30) REVERT: g 72 MET cc_start: 0.9084 (mmm) cc_final: 0.8496 (mmm) REVERT: g 143 ASP cc_start: 0.8575 (t0) cc_final: 0.8110 (t0) REVERT: F 29 MET cc_start: 0.7897 (mmm) cc_final: 0.7127 (tpp) REVERT: A 58 TYR cc_start: 0.7025 (m-80) cc_final: 0.6777 (m-80) REVERT: A 69 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7756 (mt0) REVERT: B 72 MET cc_start: 0.8935 (tpp) cc_final: 0.8371 (tpt) REVERT: C 67 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 88 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 128 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6799 (p90) REVERT: C 129 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7975 (mm-30) REVERT: C 134 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: D 29 MET cc_start: 0.8589 (mmm) cc_final: 0.8132 (tpp) REVERT: E 60 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7734 (p0) REVERT: E 145 MET cc_start: 0.9271 (ptp) cc_final: 0.8685 (pmm) REVERT: H 72 MET cc_start: 0.8537 (mmm) cc_final: 0.7635 (mmm) REVERT: H 74 GLU cc_start: 0.8973 (pm20) cc_final: 0.7759 (pm20) REVERT: H 88 GLU cc_start: 0.8772 (tp30) cc_final: 0.8540 (tp30) REVERT: H 129 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7682 (tm-30) REVERT: J 51 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8848 (tttm) REVERT: J 60 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7991 (p0) REVERT: K 55 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8899 (mm-30) REVERT: K 72 MET cc_start: 0.8315 (tpt) cc_final: 0.8021 (mmm) REVERT: K 78 GLU cc_start: 0.8761 (mp0) cc_final: 0.8215 (mp0) REVERT: K 92 GLU cc_start: 0.9196 (tp30) cc_final: 0.8975 (tp30) REVERT: K 128 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7851 (p90) REVERT: L 39 MET cc_start: 0.8602 (mtp) cc_final: 0.7763 (mtp) REVERT: M 3 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: M 72 MET cc_start: 0.9607 (mmm) cc_final: 0.8800 (mmm) REVERT: M 136 MET cc_start: 0.8997 (ppp) cc_final: 0.8718 (ppp) REVERT: N 66 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8595 (ttmm) REVERT: N 67 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8236 (p) REVERT: N 72 MET cc_start: 0.8426 (mmm) cc_final: 0.8179 (mmm) REVERT: N 74 GLU cc_start: 0.8724 (pm20) cc_final: 0.8158 (pm20) REVERT: N 129 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: N 155 GLU cc_start: 0.9327 (tp30) cc_final: 0.9109 (mp0) REVERT: O 24 ASP cc_start: 0.8759 (m-30) cc_final: 0.8515 (p0) REVERT: P 3 PHE cc_start: 0.9073 (m-80) cc_final: 0.8507 (m-80) REVERT: P 11 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: P 145 MET cc_start: 0.8957 (ttm) cc_final: 0.8555 (mtp) outliers start: 60 outliers final: 43 residues processed: 287 average time/residue: 0.1162 time to fit residues: 55.4504 Evaluate side-chains 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 135 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.045343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.036455 restraints weight = 102806.702| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.66 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 20250 Z= 0.368 Angle : 0.812 14.565 27270 Z= 0.395 Chirality : 0.047 0.228 3090 Planarity : 0.004 0.064 3486 Dihedral : 5.018 25.313 2724 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.02 % Favored : 91.67 % Rotamer: Outliers : 3.20 % Allowed : 27.68 % Favored : 69.11 % 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: -0.99 (0.16), residues: 2580 helix: 1.75 (0.29), residues: 336 sheet: -0.38 (0.16), residues: 1044 loop : -1.61 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 14 TYR 0.022 0.002 TYR I 58 PHE 0.026 0.002 PHE I 6 TRP 0.018 0.002 TRP K 65 HIS 0.005 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00807 (20244) covalent geometry : angle 0.81254 (27258) SS BOND : bond 0.00539 ( 6) SS BOND : angle 0.49507 ( 12) hydrogen bonds : bond 0.03661 ( 363) hydrogen bonds : angle 5.18084 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.26 seconds wall clock time: 52 minutes 29.29 seconds (3149.29 seconds total)