Starting phenix.real_space_refine on Tue May 20 12:02:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1j_61073/05_2025/9j1j_61073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1j_61073/05_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_61073/05_2025/9j1j_61073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1j_61073/05_2025/9j1j_61073.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1j_61073/05_2025/9j1j_61073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1j_61073/05_2025/9j1j_61073.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.33, per 1000 atoms: 0.62 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: 4.68 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.74 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: 4.63 Time building geometry restraints manager: 5.48 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.170 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- 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 : 15.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 75 HIS 0.005 0.001 HIS F 112 PHE 0.018 0.002 PHE K 128 TYR 0.013 0.001 TYR E 83 ARG 0.006 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.20678 ( 363) hydrogen bonds : angle 7.95703 ( 1026) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.40958 ( 12) covalent geometry : bond 0.00406 (20244) covalent geometry : angle 0.82575 (27258) *********************** 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 : 2.160 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: 0.2901 time to fit residues: 114.8100 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 : 2.575 ------------------------------------------------------------------------------- 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 212 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 0.0270 chunk 228 optimal weight: 9.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- 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** O 67 ASN P 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039346 restraints weight = 99473.362| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.86 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20250 Z= 0.232 Angle : 0.651 8.287 27270 Z= 0.333 Chirality : 0.045 0.165 3090 Planarity : 0.004 0.064 3486 Dihedral : 5.025 37.191 2732 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.71 % Favored : 93.02 % Rotamer: Outliers : 3.11 % Allowed : 22.88 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2580 helix: 1.26 (0.30), residues: 330 sheet: 0.07 (0.15), residues: 1056 loop : -1.75 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 65 HIS 0.006 0.001 HIS I 63 PHE 0.011 0.001 PHE H 117 TYR 0.015 0.001 TYR G 96 ARG 0.005 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 363) hydrogen bonds : angle 5.45890 ( 1026) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.31900 ( 12) covalent geometry : bond 0.00514 (20244) covalent geometry : angle 0.65138 (27258) *********************** 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 298 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 145 MET cc_start: 0.8714 (ptm) cc_final: 0.8435 (ptp) REVERT: g 72 MET cc_start: 0.9035 (mmm) cc_final: 0.8666 (mmm) REVERT: g 88 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8819 (tm-30) REVERT: g 143 ASP cc_start: 0.8267 (t0) cc_final: 0.7922 (t0) REVERT: A 16 MET cc_start: 0.8328 (tmm) cc_final: 0.7838 (tmm) REVERT: A 42 MET cc_start: 0.6823 (mmm) cc_final: 0.6521 (mmm) REVERT: B 72 MET cc_start: 0.9050 (tpp) cc_final: 0.8723 (tpt) REVERT: C 128 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7410 (p90) REVERT: C 129 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7872 (mm-30) REVERT: C 145 MET cc_start: 0.8741 (ptp) cc_final: 0.8397 (pmm) REVERT: D 29 MET cc_start: 0.8409 (mmm) cc_final: 0.7933 (tpp) REVERT: E 145 MET cc_start: 0.9165 (ptp) cc_final: 0.8599 (pmm) REVERT: H 72 MET cc_start: 0.8100 (mmm) cc_final: 0.7592 (mmm) REVERT: H 74 GLU cc_start: 0.8628 (pm20) cc_final: 0.8005 (pm20) REVERT: H 88 GLU cc_start: 0.8825 (tp30) cc_final: 0.8603 (tp30) REVERT: H 134 GLU cc_start: 0.8112 (tp30) cc_final: 0.7881 (tp30) REVERT: H 160 MET cc_start: 0.8867 (mmp) cc_final: 0.8650 (mmp) REVERT: I 83 MET cc_start: 0.8841 (tmm) cc_final: 0.8501 (tmm) REVERT: J 3 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8688 (m-10) REVERT: J 60 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8248 (p0) REVERT: J 72 MET cc_start: 0.8537 (mmm) cc_final: 0.8254 (mmm) REVERT: K 55 GLU cc_start: 0.9100 (tt0) cc_final: 0.8738 (tp30) REVERT: K 72 MET cc_start: 0.7767 (mmm) cc_final: 0.7567 (mmm) REVERT: K 92 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 150 ASP cc_start: 0.8753 (m-30) cc_final: 0.8189 (t0) REVERT: L 1 MET cc_start: 0.8952 (tmm) cc_final: 0.8742 (tmm) REVERT: M 3 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: M 72 MET cc_start: 0.9317 (mmm) cc_final: 0.8841 (mmm) REVERT: M 76 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9320 (t) REVERT: M 109 ASN cc_start: 0.9374 (t0) cc_final: 0.9171 (t0) REVERT: N 128 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7998 (p90) REVERT: O 24 ASP cc_start: 0.8760 (m-30) cc_final: 0.8449 (p0) REVERT: O 103 ASN cc_start: 0.8484 (t0) cc_final: 0.8210 (m-40) REVERT: O 116 SER cc_start: 0.8561 (t) cc_final: 0.8320 (p) REVERT: P 11 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: P 160 MET cc_start: 0.8712 (tpp) cc_final: 0.8355 (tpp) outliers start: 66 outliers final: 27 residues processed: 275 average time/residue: 0.2758 time to fit residues: 122.1486 Evaluate side-chains 254 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 29 MET 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 137 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE 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 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 N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 39 MET 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 P residue 137 THR 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 239 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.048128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039035 restraints weight = 98044.051| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.76 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1603 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= 0.217 Angle : 0.621 9.143 27270 Z= 0.316 Chirality : 0.045 0.196 3090 Planarity : 0.003 0.056 3486 Dihedral : 4.779 25.335 2724 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.02 % Favored : 92.75 % Rotamer: Outliers : 4.10 % Allowed : 23.12 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2580 helix: 1.47 (0.30), residues: 330 sheet: 0.04 (0.15), residues: 1062 loop : -1.63 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 75 HIS 0.006 0.001 HIS L 63 PHE 0.010 0.001 PHE I 6 TYR 0.009 0.001 TYR E 83 ARG 0.004 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 363) hydrogen bonds : angle 5.12637 ( 1026) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.31264 ( 12) covalent geometry : bond 0.00476 (20244) covalent geometry : angle 0.62134 (27258) *********************** 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 323 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 236 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8219 (mtmm) REVERT: g 72 MET cc_start: 0.9080 (mmm) cc_final: 0.8708 (mmm) REVERT: g 143 ASP cc_start: 0.8426 (t0) cc_final: 0.7999 (t0) REVERT: A 16 MET cc_start: 0.8373 (tmm) cc_final: 0.7905 (tmt) REVERT: A 42 MET cc_start: 0.7086 (mmm) cc_final: 0.6757 (mmm) REVERT: B 72 MET cc_start: 0.9077 (tpp) cc_final: 0.8792 (mmp) REVERT: C 128 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7308 (p90) REVERT: C 129 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7958 (mm-30) REVERT: D 7 MET cc_start: 0.9156 (tpp) cc_final: 0.8800 (tmm) REVERT: D 29 MET cc_start: 0.8555 (mmm) cc_final: 0.8025 (tpp) REVERT: H 72 MET cc_start: 0.8229 (mmm) cc_final: 0.7564 (mmm) REVERT: H 74 GLU cc_start: 0.8712 (pm20) cc_final: 0.7914 (pm20) REVERT: H 88 GLU cc_start: 0.8864 (tp30) cc_final: 0.8547 (tp30) REVERT: I 7 MET cc_start: 0.8962 (tpt) cc_final: 0.8613 (tpp) REVERT: I 83 MET cc_start: 0.8860 (tmm) cc_final: 0.8523 (tmm) REVERT: J 3 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: J 51 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8950 (tttp) REVERT: J 60 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (p0) REVERT: J 72 MET cc_start: 0.8710 (mmm) cc_final: 0.8138 (mmm) REVERT: J 150 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8877 (t0) REVERT: K 55 GLU cc_start: 0.9113 (tt0) cc_final: 0.8800 (tp30) REVERT: K 72 MET cc_start: 0.7959 (mmm) cc_final: 0.7561 (tmm) REVERT: K 78 GLU cc_start: 0.8650 (mp0) cc_final: 0.8401 (mp0) REVERT: K 128 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7887 (p90) REVERT: K 150 ASP cc_start: 0.8779 (m-30) cc_final: 0.8223 (t0) REVERT: L 1 MET cc_start: 0.8850 (tmm) cc_final: 0.8643 (tmm) REVERT: M 3 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: M 72 MET cc_start: 0.9439 (mmm) cc_final: 0.8713 (mmm) REVERT: M 76 SER cc_start: 0.9525 (OUTLIER) cc_final: 0.9282 (t) REVERT: N 74 GLU cc_start: 0.8773 (pm20) cc_final: 0.8423 (pm20) REVERT: N 128 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7939 (p90) REVERT: N 129 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: O 24 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (p0) REVERT: P 11 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: P 72 MET cc_start: 0.9247 (tpp) cc_final: 0.8777 (tpp) outliers start: 87 outliers final: 39 residues processed: 293 average time/residue: 0.2692 time to fit residues: 127.6485 Evaluate side-chains 267 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 66 LYS 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 87 LEU 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 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 77 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL 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 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 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 K residue 128 PHE 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** N 90 HIS O 108 ASN Q 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.038633 restraints weight = 99950.151| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.78 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1949 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= 0.215 Angle : 0.635 9.609 27270 Z= 0.317 Chirality : 0.045 0.187 3090 Planarity : 0.003 0.060 3486 Dihedral : 4.738 26.127 2724 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.83 % Rotamer: Outliers : 3.77 % Allowed : 24.15 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2580 helix: 1.59 (0.30), residues: 336 sheet: 0.00 (0.16), residues: 1062 loop : -1.55 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 75 HIS 0.005 0.001 HIS I 63 PHE 0.010 0.001 PHE N 117 TYR 0.010 0.001 TYR K 126 ARG 0.004 0.001 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 363) hydrogen bonds : angle 5.00535 ( 1026) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.34118 ( 12) covalent geometry : bond 0.00474 (20244) covalent geometry : angle 0.63523 (27258) *********************** 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 311 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 231 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 72 MET cc_start: 0.9146 (mmm) cc_final: 0.8628 (mmm) REVERT: g 143 ASP cc_start: 0.8491 (t0) cc_final: 0.7945 (t0) REVERT: A 16 MET cc_start: 0.8425 (tmm) cc_final: 0.7977 (tmt) REVERT: A 42 MET cc_start: 0.7279 (mmm) cc_final: 0.7012 (mmm) REVERT: B 72 MET cc_start: 0.9059 (tpp) cc_final: 0.8792 (tpt) REVERT: C 128 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7201 (p90) REVERT: C 129 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 134 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: D 29 MET cc_start: 0.8615 (mmm) cc_final: 0.8063 (tpp) REVERT: E 145 MET cc_start: 0.9193 (ptp) cc_final: 0.8570 (pmm) REVERT: H 72 MET cc_start: 0.8338 (mmm) cc_final: 0.7683 (mmm) REVERT: H 74 GLU cc_start: 0.8824 (pm20) cc_final: 0.7731 (pm20) REVERT: H 129 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7425 (tm-30) REVERT: I 7 MET cc_start: 0.8986 (tpt) cc_final: 0.8737 (tpp) REVERT: I 83 MET cc_start: 0.8845 (tmm) cc_final: 0.8553 (tmm) REVERT: J 51 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: J 60 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8263 (p0) REVERT: J 72 MET cc_start: 0.8732 (mmm) cc_final: 0.8084 (mmm) REVERT: J 150 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8880 (t0) REVERT: K 55 GLU cc_start: 0.9091 (tt0) cc_final: 0.8691 (tp30) REVERT: K 59 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7729 (mtpp) REVERT: K 72 MET cc_start: 0.8154 (mmm) cc_final: 0.7862 (mmm) REVERT: K 78 GLU cc_start: 0.8649 (mp0) cc_final: 0.8328 (mp0) REVERT: K 88 GLU cc_start: 0.8541 (tp30) cc_final: 0.8225 (tp30) REVERT: K 128 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7938 (p90) REVERT: K 150 ASP cc_start: 0.8768 (m-30) cc_final: 0.8176 (t0) REVERT: L 1 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8583 (tmm) REVERT: L 29 MET cc_start: 0.8226 (tpp) cc_final: 0.7861 (tpp) REVERT: L 39 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8078 (mtp) REVERT: M 3 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: M 72 MET cc_start: 0.9509 (mmm) cc_final: 0.8815 (mmm) REVERT: M 136 MET cc_start: 0.9028 (ppp) cc_final: 0.8722 (ppp) REVERT: N 55 GLU cc_start: 0.8977 (tp30) cc_final: 0.8497 (mm-30) REVERT: N 74 GLU cc_start: 0.8816 (pm20) cc_final: 0.8392 (pm20) REVERT: N 128 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7905 (p90) REVERT: N 129 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: O 24 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (p0) REVERT: P 11 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: P 145 MET cc_start: 0.8782 (ttm) cc_final: 0.8469 (mtp) outliers start: 80 outliers final: 40 residues processed: 285 average time/residue: 0.2824 time to fit residues: 128.5855 Evaluate side-chains 276 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 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 52 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain A residue 40 ILE 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 C residue 59 LYS 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 77 ILE 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 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 J residue 51 LYS 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 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 128 PHE 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 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 84 VAL Chi-restraints excluded: chain Q residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** N 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038057 restraints weight = 100487.097| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.77 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20250 Z= 0.234 Angle : 0.653 11.125 27270 Z= 0.324 Chirality : 0.045 0.213 3090 Planarity : 0.003 0.058 3486 Dihedral : 4.760 27.109 2724 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.25 % Favored : 92.44 % Rotamer: Outliers : 4.10 % Allowed : 24.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2580 helix: 1.72 (0.29), residues: 336 sheet: -0.05 (0.16), residues: 1062 loop : -1.53 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 75 HIS 0.004 0.001 HIS A 63 PHE 0.010 0.001 PHE I 6 TYR 0.010 0.001 TYR K 126 ARG 0.003 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 363) hydrogen bonds : angle 4.99978 ( 1026) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.37514 ( 12) covalent geometry : bond 0.00515 (20244) covalent geometry : angle 0.65317 (27258) *********************** 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 318 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 231 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 72 MET cc_start: 0.9081 (mmm) cc_final: 0.8560 (mmm) REVERT: g 88 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8636 (tm-30) REVERT: g 143 ASP cc_start: 0.8539 (t0) cc_final: 0.7930 (t0) REVERT: A 16 MET cc_start: 0.8445 (tmm) cc_final: 0.8241 (tmm) REVERT: A 39 MET cc_start: 0.8498 (mtp) cc_final: 0.8059 (mtp) REVERT: A 42 MET cc_start: 0.7327 (mmm) cc_final: 0.7068 (mmm) REVERT: A 69 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7809 (mt0) REVERT: B 72 MET cc_start: 0.9072 (tpp) cc_final: 0.8530 (tpt) REVERT: B 160 MET cc_start: 0.8220 (mmp) cc_final: 0.7995 (tpp) REVERT: C 128 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7175 (p90) REVERT: C 129 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7894 (mm-30) REVERT: C 134 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: D 7 MET cc_start: 0.9125 (tpp) cc_final: 0.8795 (tmm) REVERT: D 29 MET cc_start: 0.8663 (mmm) cc_final: 0.8174 (tpp) REVERT: D 83 MET cc_start: 0.7878 (mmp) cc_final: 0.7646 (mmp) REVERT: E 60 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (p0) REVERT: H 72 MET cc_start: 0.8389 (mmm) cc_final: 0.7778 (mmm) REVERT: H 74 GLU cc_start: 0.8914 (pm20) cc_final: 0.7779 (pm20) REVERT: H 129 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7558 (tm-30) REVERT: I 83 MET cc_start: 0.8881 (tmm) cc_final: 0.8578 (tmm) REVERT: J 3 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: J 51 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8878 (tttm) REVERT: J 60 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8181 (p0) REVERT: J 72 MET cc_start: 0.8829 (mmm) cc_final: 0.8166 (mmm) REVERT: J 150 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8880 (t0) REVERT: K 55 GLU cc_start: 0.9140 (tt0) cc_final: 0.8898 (tp30) REVERT: K 72 MET cc_start: 0.8161 (mmm) cc_final: 0.7809 (mmm) REVERT: K 78 GLU cc_start: 0.8721 (mp0) cc_final: 0.8339 (mp0) REVERT: K 88 GLU cc_start: 0.8572 (tp30) cc_final: 0.8326 (tp30) REVERT: K 128 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.7980 (p90) REVERT: L 1 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8584 (tmm) REVERT: L 29 MET cc_start: 0.8301 (tpp) cc_final: 0.7842 (tpp) REVERT: L 39 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: M 3 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: M 72 MET cc_start: 0.9567 (mmm) cc_final: 0.8724 (mmm) REVERT: M 136 MET cc_start: 0.9029 (ppp) cc_final: 0.8722 (ppp) REVERT: N 74 GLU cc_start: 0.8845 (pm20) cc_final: 0.8306 (pm20) REVERT: N 128 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7923 (p90) REVERT: N 129 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: O 24 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (p0) REVERT: P 11 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: P 72 MET cc_start: 0.9220 (tpp) cc_final: 0.8852 (tpp) outliers start: 87 outliers final: 53 residues processed: 295 average time/residue: 0.3087 time to fit residues: 148.2168 Evaluate side-chains 291 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 2.884 ------------------------------------------------------------------------------- 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 128 PHE Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain g residue 92 GLU 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 F residue 52 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain A residue 31 ASN 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 59 LYS 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 56 ILE 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 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 128 PHE 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 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 137 THR 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 206 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 143 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN D 67 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.039045 restraints weight = 99493.861| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.96 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20250 Z= 0.138 Angle : 0.601 12.529 27270 Z= 0.298 Chirality : 0.045 0.197 3090 Planarity : 0.003 0.060 3486 Dihedral : 4.450 27.121 2724 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.28 % Favored : 93.37 % Rotamer: Outliers : 3.53 % Allowed : 25.89 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2580 helix: 2.06 (0.29), residues: 336 sheet: -0.15 (0.16), residues: 1020 loop : -1.40 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 75 HIS 0.005 0.001 HIS A 112 PHE 0.014 0.001 PHE N 29 TYR 0.009 0.001 TYR E 11 ARG 0.003 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 363) hydrogen bonds : angle 4.85519 ( 1026) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.28387 ( 12) covalent geometry : bond 0.00310 (20244) covalent geometry : angle 0.60120 (27258) *********************** 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 321 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 136 MET cc_start: 0.9212 (ppp) cc_final: 0.8985 (ppp) REVERT: g 72 MET cc_start: 0.9061 (mmm) cc_final: 0.8639 (mmm) REVERT: g 143 ASP cc_start: 0.8538 (t0) cc_final: 0.7904 (t0) REVERT: F 1 MET cc_start: 0.8383 (tpt) cc_final: 0.8165 (tpt) REVERT: F 29 MET cc_start: 0.7999 (mmm) cc_final: 0.7703 (tpp) REVERT: B 72 MET cc_start: 0.9000 (tpp) cc_final: 0.8708 (tpt) REVERT: B 160 MET cc_start: 0.8141 (mmp) cc_final: 0.7842 (tpp) REVERT: C 88 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 128 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.6982 (p90) REVERT: C 129 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7899 (mm-30) REVERT: C 134 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: E 60 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 145 MET cc_start: 0.9195 (ptp) cc_final: 0.8551 (pmm) REVERT: H 72 MET cc_start: 0.8309 (mmm) cc_final: 0.7840 (mmm) REVERT: H 74 GLU cc_start: 0.8901 (pm20) cc_final: 0.7737 (pm20) REVERT: H 88 GLU cc_start: 0.8853 (tp30) cc_final: 0.8625 (tp30) REVERT: H 129 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7564 (tm-30) REVERT: I 83 MET cc_start: 0.8828 (tmm) cc_final: 0.8535 (tmm) REVERT: J 3 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: J 60 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (p0) REVERT: J 72 MET cc_start: 0.8884 (mmm) cc_final: 0.8288 (tpp) REVERT: J 150 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8831 (t0) REVERT: K 78 GLU cc_start: 0.8717 (mp0) cc_final: 0.8298 (mp0) REVERT: K 88 GLU cc_start: 0.8468 (tp30) cc_final: 0.8205 (tp30) REVERT: K 128 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7874 (p90) REVERT: L 1 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8613 (tmm) REVERT: L 29 MET cc_start: 0.8209 (tpp) cc_final: 0.7832 (tpp) REVERT: L 39 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7869 (mtp) REVERT: M 3 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: M 72 MET cc_start: 0.9524 (mmm) cc_final: 0.8716 (mmm) REVERT: N 55 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8756 (mm-30) REVERT: N 74 GLU cc_start: 0.8808 (pm20) cc_final: 0.8237 (pm20) REVERT: N 129 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: O 24 ASP cc_start: 0.8859 (m-30) cc_final: 0.8595 (p0) REVERT: P 11 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: P 145 MET cc_start: 0.9028 (ttm) cc_final: 0.8609 (mtp) REVERT: Q 160 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8252 (tpp) outliers start: 75 outliers final: 41 residues processed: 298 average time/residue: 0.2791 time to fit residues: 133.5112 Evaluate side-chains 284 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE 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 A residue 40 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 62 VAL 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 67 ASN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 125 LEU 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 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain J residue 3 PHE 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 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 55 GLU Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 13 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 176 optimal weight: 0.0570 chunk 235 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 HIS ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.048609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039351 restraints weight = 98908.884| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.96 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20250 Z= 0.133 Angle : 0.615 11.673 27270 Z= 0.303 Chirality : 0.045 0.194 3090 Planarity : 0.003 0.063 3486 Dihedral : 4.334 24.821 2724 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.12 % Favored : 93.53 % Rotamer: Outliers : 3.44 % Allowed : 26.08 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2580 helix: 2.06 (0.29), residues: 342 sheet: -0.15 (0.16), residues: 1020 loop : -1.37 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 54 HIS 0.006 0.001 HIS L 64 PHE 0.016 0.001 PHE I 6 TYR 0.010 0.001 TYR A 58 ARG 0.002 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 363) hydrogen bonds : angle 4.80676 ( 1026) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.27397 ( 12) covalent geometry : bond 0.00301 (20244) covalent geometry : angle 0.61480 (27258) *********************** 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 317 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 136 MET cc_start: 0.9135 (ppp) cc_final: 0.8901 (ppp) REVERT: g 72 MET cc_start: 0.9095 (mmm) cc_final: 0.8664 (mmm) REVERT: g 143 ASP cc_start: 0.8538 (t0) cc_final: 0.8031 (t0) REVERT: F 29 MET cc_start: 0.8091 (mmm) cc_final: 0.7781 (tpp) REVERT: A 58 TYR cc_start: 0.6745 (m-80) cc_final: 0.6224 (m-80) REVERT: A 69 GLN cc_start: 0.8410 (tp-100) cc_final: 0.7509 (mt0) REVERT: B 72 MET cc_start: 0.8970 (tpp) cc_final: 0.8394 (tpt) REVERT: B 160 MET cc_start: 0.8167 (mmp) cc_final: 0.7853 (tpp) REVERT: C 128 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6997 (p90) REVERT: C 129 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 134 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 29 MET cc_start: 0.8583 (mmm) cc_final: 0.8154 (tpt) REVERT: D 101 LYS cc_start: 0.8568 (mppt) cc_final: 0.8341 (mmmt) REVERT: E 60 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7791 (p0) REVERT: E 145 MET cc_start: 0.9254 (ptp) cc_final: 0.8508 (pmm) REVERT: H 72 MET cc_start: 0.8358 (mmm) cc_final: 0.7867 (mmm) REVERT: H 74 GLU cc_start: 0.8861 (pm20) cc_final: 0.7693 (pm20) REVERT: H 88 GLU cc_start: 0.8789 (tp30) cc_final: 0.8551 (tp30) REVERT: H 129 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7208 (tm-30) REVERT: I 1 MET cc_start: 0.8050 (tmm) cc_final: 0.7825 (tmm) REVERT: I 83 MET cc_start: 0.8809 (tmm) cc_final: 0.8500 (tmm) REVERT: J 3 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: J 51 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8972 (tttm) REVERT: J 60 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8105 (p0) REVERT: J 72 MET cc_start: 0.8872 (mmm) cc_final: 0.8174 (mmm) REVERT: J 150 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8802 (t0) REVERT: K 55 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8962 (mm-30) REVERT: K 72 MET cc_start: 0.7740 (mmm) cc_final: 0.7386 (tmm) REVERT: K 78 GLU cc_start: 0.8693 (mp0) cc_final: 0.8242 (mp0) REVERT: K 88 GLU cc_start: 0.8482 (tp30) cc_final: 0.8200 (tp30) REVERT: K 128 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7842 (p90) REVERT: L 1 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8606 (tmm) REVERT: L 29 MET cc_start: 0.8324 (tpp) cc_final: 0.7905 (tpp) REVERT: L 39 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: M 3 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: M 72 MET cc_start: 0.9545 (mmm) cc_final: 0.8712 (mmm) REVERT: N 55 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mm-30) REVERT: N 74 GLU cc_start: 0.8796 (pm20) cc_final: 0.8183 (pm20) REVERT: N 129 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: O 24 ASP cc_start: 0.8842 (m-30) cc_final: 0.8599 (p0) REVERT: P 11 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: Q 78 GLU cc_start: 0.7874 (tp30) cc_final: 0.7654 (tp30) REVERT: Q 145 MET cc_start: 0.8783 (mtp) cc_final: 0.8298 (tpp) REVERT: Q 160 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7851 (tpp) outliers start: 73 outliers final: 38 residues processed: 293 average time/residue: 0.2669 time to fit residues: 125.6745 Evaluate side-chains 286 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE 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 50 SER Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 62 VAL 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 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 56 ILE Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR 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 K residue 55 GLU 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 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 50 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU 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 84 VAL Chi-restraints excluded: chain Q residue 108 ILE 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 69 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.037253 restraints weight = 102116.280| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.76 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20250 Z= 0.310 Angle : 0.746 11.971 27270 Z= 0.367 Chirality : 0.046 0.214 3090 Planarity : 0.003 0.069 3486 Dihedral : 4.896 31.611 2724 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.40 % Favored : 92.29 % Rotamer: Outliers : 3.44 % Allowed : 26.08 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2580 helix: 1.86 (0.29), residues: 336 sheet: -0.17 (0.16), residues: 1044 loop : -1.48 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 65 HIS 0.007 0.001 HIS L 64 PHE 0.022 0.002 PHE I 6 TYR 0.019 0.002 TYR I 58 ARG 0.008 0.001 ARG O 14 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 363) hydrogen bonds : angle 5.04808 ( 1026) SS BOND : bond 0.00431 ( 6) SS BOND : angle 0.41511 ( 12) covalent geometry : bond 0.00682 (20244) covalent geometry : angle 0.74594 (27258) *********************** 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 295 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 222 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9582 (mm) cc_final: 0.9371 (mm) REVERT: G 136 MET cc_start: 0.9224 (ppp) cc_final: 0.8984 (ppp) REVERT: g 72 MET cc_start: 0.9131 (mmm) cc_final: 0.8524 (mmm) REVERT: g 143 ASP cc_start: 0.8612 (t0) cc_final: 0.8157 (t0) REVERT: F 29 MET cc_start: 0.8341 (mmm) cc_final: 0.7897 (tpp) REVERT: A 69 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7860 (mt0) REVERT: B 128 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8571 (p90) REVERT: C 128 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7060 (p90) REVERT: C 129 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7885 (mm-30) REVERT: C 134 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: D 29 MET cc_start: 0.8619 (mmm) cc_final: 0.8392 (tpp) REVERT: E 60 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7851 (p0) REVERT: H 74 GLU cc_start: 0.8997 (pm20) cc_final: 0.8129 (pm20) REVERT: H 88 GLU cc_start: 0.8959 (tp30) cc_final: 0.8638 (tp30) REVERT: H 134 GLU cc_start: 0.7911 (tp30) cc_final: 0.7687 (tp30) REVERT: I 83 MET cc_start: 0.8840 (tmm) cc_final: 0.8512 (tmm) REVERT: J 3 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: J 51 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8783 (tttm) REVERT: J 60 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8425 (p0) REVERT: K 55 GLU cc_start: 0.9316 (tp30) cc_final: 0.8872 (tp30) REVERT: K 72 MET cc_start: 0.7981 (mmm) cc_final: 0.7601 (tmm) REVERT: K 78 GLU cc_start: 0.8758 (mp0) cc_final: 0.8300 (mp0) REVERT: K 88 GLU cc_start: 0.8726 (tp30) cc_final: 0.8495 (tp30) REVERT: K 128 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8069 (p90) REVERT: L 1 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8598 (tmm) REVERT: L 29 MET cc_start: 0.8406 (tpp) cc_final: 0.8043 (tpp) REVERT: M 72 MET cc_start: 0.9591 (mmm) cc_final: 0.8601 (mmm) REVERT: M 136 MET cc_start: 0.9051 (ppp) cc_final: 0.8739 (ppp) REVERT: N 74 GLU cc_start: 0.8844 (pm20) cc_final: 0.8281 (pm20) REVERT: N 128 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8174 (p90) REVERT: N 129 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: O 24 ASP cc_start: 0.8883 (m-30) cc_final: 0.8601 (p0) REVERT: P 11 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: Q 78 GLU cc_start: 0.7923 (tp30) cc_final: 0.7675 (tp30) outliers start: 73 outliers final: 47 residues processed: 279 average time/residue: 0.2768 time to fit residues: 124.1512 Evaluate side-chains 274 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 128 PHE 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 A residue 40 ILE Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 59 LYS 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 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 128 PHE Chi-restraints excluded: chain H residue 137 THR 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 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 86 ILE 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 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 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 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 207 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 51 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.046916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.037930 restraints weight = 100334.889| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.72 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20250 Z= 0.226 Angle : 0.687 11.535 27270 Z= 0.337 Chirality : 0.046 0.185 3090 Planarity : 0.003 0.073 3486 Dihedral : 4.738 28.214 2724 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.94 % Favored : 92.75 % Rotamer: Outliers : 3.30 % Allowed : 26.27 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2580 helix: 1.94 (0.29), residues: 336 sheet: -0.17 (0.16), residues: 1050 loop : -1.56 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 65 HIS 0.005 0.001 HIS L 64 PHE 0.019 0.001 PHE I 6 TYR 0.013 0.001 TYR A 58 ARG 0.006 0.000 ARG O 14 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 363) hydrogen bonds : angle 4.96943 ( 1026) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.37367 ( 12) covalent geometry : bond 0.00503 (20244) covalent geometry : angle 0.68674 (27258) *********************** 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 301 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 231 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9576 (mm) cc_final: 0.9367 (mm) REVERT: G 136 MET cc_start: 0.9184 (ppp) cc_final: 0.8958 (ppp) REVERT: g 72 MET cc_start: 0.9142 (mmm) cc_final: 0.8619 (mmm) REVERT: g 143 ASP cc_start: 0.8572 (t0) cc_final: 0.8101 (t0) REVERT: g 160 MET cc_start: 0.8703 (mmm) cc_final: 0.8385 (mmt) REVERT: F 29 MET cc_start: 0.8331 (mmm) cc_final: 0.7875 (tpp) REVERT: A 69 GLN cc_start: 0.8553 (tp-100) cc_final: 0.7749 (mt0) REVERT: B 72 MET cc_start: 0.9038 (tpp) cc_final: 0.8495 (tpt) REVERT: C 128 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.6951 (p90) REVERT: C 129 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 134 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: D 29 MET cc_start: 0.8595 (mmm) cc_final: 0.8331 (tpp) REVERT: E 60 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7797 (p0) REVERT: E 72 MET cc_start: 0.8839 (mmm) cc_final: 0.7914 (tpp) REVERT: H 72 MET cc_start: 0.8448 (mmm) cc_final: 0.7799 (mmm) REVERT: H 74 GLU cc_start: 0.9042 (pm20) cc_final: 0.7774 (pm20) REVERT: H 88 GLU cc_start: 0.8921 (tp30) cc_final: 0.8701 (tp30) REVERT: H 129 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7665 (tm-30) REVERT: H 134 GLU cc_start: 0.7841 (tp30) cc_final: 0.7629 (tp30) REVERT: I 41 GLU cc_start: 0.8274 (tt0) cc_final: 0.7796 (pt0) REVERT: I 83 MET cc_start: 0.8837 (tmm) cc_final: 0.8530 (tmm) REVERT: J 3 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: J 51 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8821 (tttm) REVERT: J 60 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8361 (p0) REVERT: J 136 MET cc_start: 0.9481 (ttp) cc_final: 0.9271 (ttp) REVERT: K 55 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: K 72 MET cc_start: 0.7925 (mmm) cc_final: 0.7640 (tmm) REVERT: K 78 GLU cc_start: 0.8740 (mp0) cc_final: 0.8269 (mp0) REVERT: K 88 GLU cc_start: 0.8647 (tp30) cc_final: 0.8414 (tp30) REVERT: K 128 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8025 (p90) REVERT: L 39 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8061 (mtp) REVERT: M 72 MET cc_start: 0.9596 (mmm) cc_final: 0.8668 (mmm) REVERT: M 136 MET cc_start: 0.9013 (ppp) cc_final: 0.8691 (ppp) REVERT: N 74 GLU cc_start: 0.8806 (pm20) cc_final: 0.8208 (pm20) REVERT: N 128 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8034 (p90) REVERT: N 129 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: O 24 ASP cc_start: 0.8838 (m-30) cc_final: 0.8576 (p0) REVERT: P 11 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: P 145 MET cc_start: 0.8950 (ttm) cc_final: 0.8450 (mtp) REVERT: Q 78 GLU cc_start: 0.7954 (tp30) cc_final: 0.7723 (tp30) REVERT: Q 134 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7910 (tp30) REVERT: Q 145 MET cc_start: 0.8910 (mmm) cc_final: 0.8577 (mmm) outliers start: 70 outliers final: 48 residues processed: 281 average time/residue: 0.2706 time to fit residues: 123.6335 Evaluate side-chains 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 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 A residue 40 ILE Chi-restraints excluded: chain B residue 3 PHE 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 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 145 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 39 MET 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 128 PHE Chi-restraints excluded: chain N residue 129 GLU 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 3 PHE 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 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 190 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 219 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 166 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.048112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039012 restraints weight = 99510.185| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.85 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20250 Z= 0.141 Angle : 0.658 12.443 27270 Z= 0.322 Chirality : 0.045 0.188 3090 Planarity : 0.003 0.066 3486 Dihedral : 4.470 29.398 2724 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.86 % Favored : 92.83 % Rotamer: Outliers : 2.78 % Allowed : 27.17 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2580 helix: 2.04 (0.29), residues: 342 sheet: -0.26 (0.16), residues: 1008 loop : -1.45 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 75 HIS 0.005 0.001 HIS A 112 PHE 0.016 0.001 PHE I 6 TYR 0.014 0.001 TYR A 58 ARG 0.006 0.000 ARG O 14 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 363) hydrogen bonds : angle 4.88767 ( 1026) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.34309 ( 12) covalent geometry : bond 0.00324 (20244) covalent geometry : angle 0.65817 (27258) ********************** 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 302 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9546 (mm) cc_final: 0.9333 (mm) REVERT: G 136 MET cc_start: 0.9140 (ppp) cc_final: 0.8909 (ppp) REVERT: g 72 MET cc_start: 0.9101 (mmm) cc_final: 0.8573 (mmm) REVERT: g 143 ASP cc_start: 0.8531 (t0) cc_final: 0.8078 (t0) REVERT: F 29 MET cc_start: 0.8244 (mmm) cc_final: 0.7812 (tpp) REVERT: A 35 MET cc_start: 0.8273 (ptp) cc_final: 0.7951 (ptp) REVERT: A 69 GLN cc_start: 0.8518 (tp-100) cc_final: 0.7647 (mt0) REVERT: B 72 MET cc_start: 0.8975 (tpp) cc_final: 0.8387 (tpt) REVERT: C 128 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6946 (p90) REVERT: C 129 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 134 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 29 MET cc_start: 0.8575 (mmm) cc_final: 0.8226 (tpp) REVERT: E 60 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7762 (p0) REVERT: E 72 MET cc_start: 0.8800 (mmm) cc_final: 0.7776 (tpp) REVERT: E 145 MET cc_start: 0.9254 (ptp) cc_final: 0.8578 (pmm) REVERT: H 72 MET cc_start: 0.8344 (mmm) cc_final: 0.7748 (mmm) REVERT: H 74 GLU cc_start: 0.8955 (pm20) cc_final: 0.7740 (pm20) REVERT: H 88 GLU cc_start: 0.8796 (tp30) cc_final: 0.8572 (tp30) REVERT: I 41 GLU cc_start: 0.8208 (tt0) cc_final: 0.7801 (pt0) REVERT: I 83 MET cc_start: 0.8827 (tmm) cc_final: 0.8513 (tmm) REVERT: J 3 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: J 51 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8910 (tttm) REVERT: J 60 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8236 (p0) REVERT: J 136 MET cc_start: 0.9371 (ttp) cc_final: 0.8387 (tmm) REVERT: K 55 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8900 (mm-30) REVERT: K 72 MET cc_start: 0.7929 (mmm) cc_final: 0.7438 (tmm) REVERT: K 78 GLU cc_start: 0.8703 (mp0) cc_final: 0.8224 (mp0) REVERT: K 88 GLU cc_start: 0.8546 (tp30) cc_final: 0.8289 (tp30) REVERT: K 128 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.7915 (p90) REVERT: L 39 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: L 58 TYR cc_start: 0.7317 (m-80) cc_final: 0.6909 (m-80) REVERT: M 3 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: M 72 MET cc_start: 0.9604 (mmm) cc_final: 0.8775 (mmm) REVERT: M 136 MET cc_start: 0.8926 (ppp) cc_final: 0.8620 (ppp) REVERT: N 74 GLU cc_start: 0.8766 (pm20) cc_final: 0.8137 (pm20) REVERT: N 128 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7976 (p90) REVERT: N 129 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: O 24 ASP cc_start: 0.8806 (m-30) cc_final: 0.8521 (p0) REVERT: P 11 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: P 145 MET cc_start: 0.8983 (ttm) cc_final: 0.8680 (mtp) REVERT: Q 78 GLU cc_start: 0.7924 (tp30) cc_final: 0.7707 (tp30) REVERT: Q 134 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7962 (tp30) REVERT: Q 145 MET cc_start: 0.8827 (mmm) cc_final: 0.8499 (mmm) outliers start: 59 outliers final: 40 residues processed: 281 average time/residue: 0.2838 time to fit residues: 130.1614 Evaluate side-chains 284 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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 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 B residue 3 PHE 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 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 128 PHE Chi-restraints excluded: chain H residue 137 THR 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 145 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 39 MET 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 128 PHE Chi-restraints excluded: chain N residue 129 GLU 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 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 94 optimal weight: 0.0020 chunk 213 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- 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 51 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.047523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038517 restraints weight = 100349.558| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.75 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20250 Z= 0.189 Angle : 0.674 12.578 27270 Z= 0.331 Chirality : 0.045 0.179 3090 Planarity : 0.003 0.052 3486 Dihedral : 4.495 28.796 2724 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.90 % Favored : 92.79 % Rotamer: Outliers : 2.87 % Allowed : 27.07 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2580 helix: 2.20 (0.29), residues: 336 sheet: -0.10 (0.16), residues: 1050 loop : -1.51 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 54 HIS 0.005 0.001 HIS L 64 PHE 0.015 0.001 PHE I 6 TYR 0.012 0.001 TYR I 58 ARG 0.006 0.000 ARG O 14 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 363) hydrogen bonds : angle 4.93472 ( 1026) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.35442 ( 12) covalent geometry : bond 0.00427 (20244) covalent geometry : angle 0.67406 (27258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5986.76 seconds wall clock time: 106 minutes 26.50 seconds (6386.50 seconds total)