Starting phenix.real_space_refine on Tue Jun 17 12:10:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1j_61073/06_2025/9j1j_61073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1j_61073/06_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_61073/06_2025/9j1j_61073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1j_61073/06_2025/9j1j_61073.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1j_61073/06_2025/9j1j_61073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1j_61073/06_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-5710/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: 11.38, per 1000 atoms: 0.57 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: 4.50 Conformation dependent library (CDL) restraints added in 2.3 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: 1.64 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: 4.40 Time building geometry restraints manager: 5.36 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.510 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- 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 : 2.674 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: 0.2831 time to fit residues: 112.4234 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 : 2.336 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039347 restraints weight = 99473.364| |-----------------------------------------------------------------------------| 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 : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 145 MET cc_start: 0.8715 (ptm) cc_final: 0.8436 (ptp) REVERT: g 72 MET cc_start: 0.9034 (mmm) cc_final: 0.8665 (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: 0.7921 (t0) REVERT: A 16 MET cc_start: 0.8329 (tmm) cc_final: 0.7839 (tmm) REVERT: A 42 MET cc_start: 0.6823 (mmm) cc_final: 0.6520 (mmm) REVERT: B 72 MET cc_start: 0.9051 (tpp) cc_final: 0.8724 (tpt) REVERT: C 128 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7409 (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: 0.8396 (pmm) REVERT: D 29 MET cc_start: 0.8409 (mmm) cc_final: 0.7934 (tpp) REVERT: E 145 MET cc_start: 0.9165 (ptp) cc_final: 0.8599 (pmm) REVERT: H 72 MET cc_start: 0.8097 (mmm) cc_final: 0.7590 (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: 0.8602 (tp30) REVERT: H 134 GLU cc_start: 0.8110 (tp30) cc_final: 0.7880 (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: 0.8689 (m-10) REVERT: J 60 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8248 (p0) REVERT: J 72 MET cc_start: 0.8536 (mmm) cc_final: 0.8254 (mmm) REVERT: K 55 GLU cc_start: 0.9099 (tt0) cc_final: 0.8738 (tp30) REVERT: K 72 MET cc_start: 0.7769 (mmm) cc_final: 0.7568 (mmm) REVERT: K 92 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 150 ASP cc_start: 0.8752 (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: 0.9318 (mmm) cc_final: 0.8842 (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: 0.8532 (OUTLIER) cc_final: 0.7999 (p90) REVERT: O 24 ASP cc_start: 0.8761 (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: 0.2763 time to fit residues: 122.7840 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 : 2.215 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9980 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.048229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039083 restraints weight = 98240.165| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.79 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20250 Z= 0.207 Angle : 0.614 8.960 27270 Z= 0.312 Chirality : 0.045 0.198 3090 Planarity : 0.003 0.055 3486 Dihedral : 4.739 25.145 2724 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 4.00 % Allowed : 23.35 % Favored : 72.65 % 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 (0.16), residues: 2580 helix: 1.50 (0.30), residues: 330 sheet: 0.04 (0.15), residues: 1068 loop : -1.61 (0.17), residues: 1182 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 0.009 0.001 PHE P 3 TYR 0.009 0.001 TYR E 83 ARG 0.003 0.001 ARG O 8 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 363) hydrogen bonds : angle 5.09741 ( 1026) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.30708 ( 12) covalent geometry : bond 0.00455 (20244) covalent geometry : angle 0.61434 (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 324 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: g 72 MET cc_start: 0.9076 (mmm) cc_final: 0.8706 (mmm) REVERT: g 143 ASP cc_start: 0.8426 (t0) cc_final: 0.7993 (t0) REVERT: A 16 MET cc_start: 0.8383 (tmm) cc_final: 0.7913 (tmt) REVERT: A 42 MET cc_start: 0.7062 (mmm) cc_final: 0.6737 (mmm) REVERT: B 72 MET cc_start: 0.9070 (tpp) cc_final: 0.8770 (tpt) REVERT: C 128 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7283 (p90) REVERT: C 129 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7938 (mm-30) REVERT: D 7 MET cc_start: 0.9159 (tpp) cc_final: 0.8803 (tmm) REVERT: D 29 MET cc_start: 0.8566 (mmm) cc_final: 0.8015 (tpp) REVERT: H 72 MET cc_start: 0.8205 (mmm) cc_final: 0.7551 (mmm) REVERT: H 74 GLU cc_start: 0.8695 (pm20) cc_final: 0.7908 (pm20) REVERT: H 88 GLU cc_start: 0.8855 (tp30) cc_final: 0.8538 (tp30) REVERT: I 7 MET cc_start: 0.8972 (tpt) cc_final: 0.8649 (tpp) REVERT: I 83 MET cc_start: 0.8844 (tmm) cc_final: 0.8526 (tmm) REVERT: J 51 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8957 (tttp) REVERT: J 60 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8414 (p0) REVERT: J 72 MET cc_start: 0.8709 (mmm) cc_final: 0.8132 (mmm) REVERT: J 150 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8875 (t0) REVERT: K 55 GLU cc_start: 0.9126 (tt0) cc_final: 0.8809 (tp30) REVERT: K 59 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7552 (mtpp) REVERT: K 72 MET cc_start: 0.7952 (mmm) cc_final: 0.7562 (tmm) REVERT: K 78 GLU cc_start: 0.8617 (mp0) cc_final: 0.8375 (mp0) REVERT: K 128 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7926 (p90) REVERT: K 150 ASP cc_start: 0.8780 (m-30) cc_final: 0.8220 (t0) REVERT: L 1 MET cc_start: 0.8842 (tmm) cc_final: 0.8631 (tmm) REVERT: L 29 MET cc_start: 0.8230 (tpp) cc_final: 0.7939 (tpp) REVERT: M 3 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: M 72 MET cc_start: 0.9447 (mmm) cc_final: 0.8722 (mmm) REVERT: M 76 SER cc_start: 0.9523 (OUTLIER) cc_final: 0.9281 (t) REVERT: N 74 GLU cc_start: 0.8753 (pm20) cc_final: 0.8423 (pm20) REVERT: N 128 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7905 (p90) REVERT: N 129 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: O 24 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8529 (p0) REVERT: P 11 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: P 72 MET cc_start: 0.9249 (tpp) cc_final: 0.8776 (tpp) outliers start: 85 outliers final: 38 residues processed: 294 average time/residue: 0.2775 time to fit residues: 131.4803 Evaluate side-chains 268 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 84 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 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 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: 9.9990 chunk 26 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Q 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037658 restraints weight = 101048.404| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 4.76 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 20250 Z= 0.299 Angle : 0.713 11.737 27270 Z= 0.354 Chirality : 0.046 0.185 3090 Planarity : 0.003 0.063 3486 Dihedral : 5.007 28.588 2724 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 4.19 % Allowed : 23.92 % Favored : 71.89 % 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: -0.83 (0.16), residues: 2580 helix: 1.44 (0.29), residues: 336 sheet: -0.06 (0.16), residues: 1062 loop : -1.60 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 65 HIS 0.006 0.001 HIS I 63 PHE 0.012 0.002 PHE N 117 TYR 0.014 0.002 TYR K 126 ARG 0.004 0.001 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 363) hydrogen bonds : angle 5.14013 ( 1026) SS BOND : bond 0.00436 ( 6) SS BOND : angle 0.42532 ( 12) covalent geometry : bond 0.00653 (20244) covalent geometry : angle 0.71297 (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 312 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 223 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8092 (mtmm) REVERT: g 72 MET cc_start: 0.9197 (mmm) cc_final: 0.8560 (mmm) REVERT: g 143 ASP cc_start: 0.8520 (t0) cc_final: 0.7969 (t0) REVERT: A 16 MET cc_start: 0.8436 (tmm) cc_final: 0.7834 (tmt) REVERT: A 42 MET cc_start: 0.7443 (mmm) cc_final: 0.7115 (mmm) REVERT: A 58 TYR cc_start: 0.7028 (m-80) cc_final: 0.6799 (m-80) REVERT: B 72 MET cc_start: 0.9072 (tpp) cc_final: 0.8523 (tpt) REVERT: C 128 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7177 (p90) REVERT: C 129 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 134 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: D 7 MET cc_start: 0.9144 (tpp) cc_final: 0.8820 (tmm) REVERT: D 29 MET cc_start: 0.8630 (mmm) cc_final: 0.8130 (tpp) REVERT: E 145 MET cc_start: 0.9175 (ptp) cc_final: 0.8556 (pmm) REVERT: H 66 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8459 (mttp) REVERT: H 74 GLU cc_start: 0.8916 (pm20) cc_final: 0.8106 (pm20) REVERT: I 7 MET cc_start: 0.8975 (tpt) cc_final: 0.8738 (tpp) REVERT: I 83 MET cc_start: 0.8844 (tmm) cc_final: 0.8551 (tmm) REVERT: J 3 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: J 51 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8795 (tttm) REVERT: J 60 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8147 (p0) REVERT: J 72 MET cc_start: 0.8781 (mmm) cc_final: 0.8022 (mmm) REVERT: J 150 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8892 (t0) REVERT: K 72 MET cc_start: 0.8160 (mmm) cc_final: 0.7901 (mmm) REVERT: K 78 GLU cc_start: 0.8719 (mp0) cc_final: 0.8385 (mp0) REVERT: K 88 GLU cc_start: 0.8637 (tp30) cc_final: 0.8406 (tp30) REVERT: K 128 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8013 (p90) REVERT: K 150 ASP cc_start: 0.8766 (m-30) cc_final: 0.8198 (t0) REVERT: L 1 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8546 (tmm) REVERT: M 72 MET cc_start: 0.9527 (mmm) cc_final: 0.8674 (mmm) REVERT: N 74 GLU cc_start: 0.8852 (pm20) cc_final: 0.8403 (pm20) REVERT: N 128 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7966 (p90) REVERT: N 129 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: O 24 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8588 (p0) REVERT: P 11 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: P 145 MET cc_start: 0.8875 (ttm) cc_final: 0.8530 (mtp) outliers start: 89 outliers final: 49 residues processed: 289 average time/residue: 0.2813 time to fit residues: 130.2811 Evaluate side-chains 276 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 129 GLU Chi-restraints excluded: chain g residue 132 PHE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 87 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 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 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 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain 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 59 LYS Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain 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 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: 8.9990 chunk 194 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN F 69 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** N 79 ASN O 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039559 restraints weight = 98493.341| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.99 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20250 Z= 0.113 Angle : 0.590 12.215 27270 Z= 0.294 Chirality : 0.045 0.200 3090 Planarity : 0.003 0.054 3486 Dihedral : 4.437 24.172 2724 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.81 % Favored : 93.88 % Rotamer: Outliers : 3.01 % Allowed : 26.18 % Favored : 70.81 % 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 (0.16), residues: 2580 helix: 1.93 (0.30), residues: 336 sheet: -0.13 (0.16), residues: 1026 loop : -1.39 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.005 0.001 HIS I 112 PHE 0.015 0.001 PHE N 29 TYR 0.009 0.001 TYR E 11 ARG 0.003 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 363) hydrogen bonds : angle 4.89427 ( 1026) SS BOND : bond 0.00071 ( 6) SS BOND : angle 0.28344 ( 12) covalent geometry : bond 0.00256 (20244) covalent geometry : angle 0.59034 (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 317 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 136 MET cc_start: 0.9248 (ppp) cc_final: 0.8776 (ppp) REVERT: g 72 MET cc_start: 0.8960 (mmm) cc_final: 0.8683 (mmm) REVERT: g 88 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8553 (tm-30) REVERT: g 143 ASP cc_start: 0.8493 (t0) cc_final: 0.7890 (t0) REVERT: A 69 GLN cc_start: 0.8444 (tp-100) cc_final: 0.7535 (mt0) REVERT: B 72 MET cc_start: 0.9036 (tpp) cc_final: 0.8731 (tpt) REVERT: C 88 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 128 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6912 (p90) REVERT: C 129 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7900 (mm-30) REVERT: C 134 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: D 83 MET cc_start: 0.7871 (mmp) cc_final: 0.7638 (mmp) REVERT: E 60 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7784 (p0) REVERT: E 145 MET cc_start: 0.9220 (ptp) cc_final: 0.8485 (pmm) REVERT: H 72 MET cc_start: 0.8098 (mmm) cc_final: 0.7385 (mmm) REVERT: H 74 GLU cc_start: 0.8810 (pm20) cc_final: 0.7710 (pm20) REVERT: H 88 GLU cc_start: 0.8832 (tp30) cc_final: 0.8608 (tp30) REVERT: H 129 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7564 (tm-30) REVERT: I 83 MET cc_start: 0.8832 (tmm) cc_final: 0.8536 (tmm) REVERT: J 3 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: J 60 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8025 (p0) REVERT: J 72 MET cc_start: 0.8818 (mmm) cc_final: 0.8182 (mmm) REVERT: J 150 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8843 (t0) REVERT: K 59 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: K 78 GLU cc_start: 0.8689 (mp0) cc_final: 0.8295 (mp0) REVERT: K 88 GLU cc_start: 0.8455 (tp30) cc_final: 0.8189 (tp30) REVERT: K 128 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7843 (p90) REVERT: L 1 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8608 (tmm) REVERT: L 107 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: M 3 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: M 72 MET cc_start: 0.9533 (mmm) cc_final: 0.8860 (mmm) REVERT: N 55 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8624 (mm-30) REVERT: N 74 GLU cc_start: 0.8803 (pm20) cc_final: 0.8266 (pm20) REVERT: N 129 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8463 (pm20) REVERT: O 24 ASP cc_start: 0.8805 (m-30) cc_final: 0.8537 (p0) REVERT: P 11 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: P 72 MET cc_start: 0.9281 (tpp) cc_final: 0.8816 (tpp) REVERT: P 145 MET cc_start: 0.8923 (ttm) cc_final: 0.8552 (mtp) REVERT: Q 160 MET cc_start: 0.8574 (tpp) cc_final: 0.8352 (tpp) outliers start: 64 outliers final: 29 residues processed: 295 average time/residue: 0.3280 time to fit residues: 158.4891 Evaluate side-chains 276 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 57 THR 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 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 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 125 LEU 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 59 LYS Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 206 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN ** 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 = 0.3122 r_free = 0.3122 target = 0.047039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.037935 restraints weight = 100941.095| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 4.76 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20250 Z= 0.256 Angle : 0.673 12.078 27270 Z= 0.333 Chirality : 0.045 0.184 3090 Planarity : 0.003 0.067 3486 Dihedral : 4.714 27.063 2724 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.25 % Favored : 92.40 % Rotamer: Outliers : 3.81 % Allowed : 25.85 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.29), residues: 336 sheet: -0.05 (0.16), residues: 1062 loop : -1.49 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 75 HIS 0.004 0.001 HIS A 112 PHE 0.012 0.001 PHE N 117 TYR 0.011 0.001 TYR K 126 ARG 0.003 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 363) hydrogen bonds : angle 4.92371 ( 1026) SS BOND : bond 0.00363 ( 6) SS BOND : angle 0.37622 ( 12) covalent geometry : bond 0.00561 (20244) covalent geometry : angle 0.67357 (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 307 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 226 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9596 (mm) cc_final: 0.9369 (mm) REVERT: G 136 MET cc_start: 0.9234 (ppp) cc_final: 0.8994 (ppp) REVERT: g 72 MET cc_start: 0.8881 (mmm) cc_final: 0.8571 (mmm) REVERT: g 143 ASP cc_start: 0.8546 (t0) cc_final: 0.8062 (t0) REVERT: F 29 MET cc_start: 0.8151 (mmm) cc_final: 0.7793 (tpp) REVERT: A 39 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7386 (mtp) REVERT: A 58 TYR cc_start: 0.7107 (m-80) cc_final: 0.6738 (m-80) REVERT: B 72 MET cc_start: 0.9053 (tpp) cc_final: 0.8494 (tpt) REVERT: C 128 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6989 (p90) REVERT: C 129 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 134 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 7 MET cc_start: 0.9131 (tpp) cc_final: 0.8795 (tmm) REVERT: D 29 MET cc_start: 0.8642 (mmm) cc_final: 0.8331 (tpp) REVERT: E 60 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7882 (p0) REVERT: E 145 MET cc_start: 0.9244 (ptp) cc_final: 0.9027 (ptp) REVERT: H 74 GLU cc_start: 0.8933 (pm20) cc_final: 0.8069 (pm20) REVERT: H 88 GLU cc_start: 0.8914 (tp30) cc_final: 0.8622 (tp30) REVERT: I 7 MET cc_start: 0.8961 (tpt) cc_final: 0.8519 (tpp) REVERT: I 83 MET cc_start: 0.8844 (tmm) cc_final: 0.8535 (tmm) REVERT: J 3 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: J 51 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8866 (tttm) REVERT: J 60 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8235 (p0) REVERT: J 72 MET cc_start: 0.8852 (mmm) cc_final: 0.8132 (mmm) REVERT: J 150 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8841 (t0) REVERT: K 55 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8845 (tp30) REVERT: K 72 MET cc_start: 0.8143 (mmm) cc_final: 0.7655 (tmm) REVERT: K 78 GLU cc_start: 0.8733 (mp0) cc_final: 0.8422 (mp0) REVERT: K 88 GLU cc_start: 0.8615 (tp30) cc_final: 0.8398 (tp30) REVERT: K 128 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8021 (p90) REVERT: L 1 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8606 (tmm) REVERT: M 3 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: M 72 MET cc_start: 0.9580 (mmm) cc_final: 0.8637 (mmm) REVERT: M 136 MET cc_start: 0.9034 (ppp) cc_final: 0.8729 (ppp) REVERT: N 74 GLU cc_start: 0.8829 (pm20) cc_final: 0.8289 (pm20) REVERT: N 128 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8116 (p90) REVERT: N 129 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: O 24 ASP cc_start: 0.8856 (m-30) cc_final: 0.8608 (p0) REVERT: P 11 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7961 (m-80) outliers start: 81 outliers final: 42 residues processed: 285 average time/residue: 0.3993 time to fit residues: 185.8023 Evaluate side-chains 269 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 50 SER Chi-restraints excluded: chain g residue 57 THR 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 39 MET 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 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 56 ILE Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 66 THR 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 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 13 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** J 90 HIS M 90 HIS ** 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 = 0.3193 r_free = 0.3193 target = 0.049517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.040274 restraints weight = 97719.604| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.96 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20250 Z= 0.106 Angle : 0.603 10.847 27270 Z= 0.301 Chirality : 0.045 0.173 3090 Planarity : 0.003 0.060 3486 Dihedral : 4.225 24.765 2724 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.16 % Favored : 94.50 % Rotamer: Outliers : 3.01 % Allowed : 26.65 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2580 helix: 2.05 (0.29), residues: 342 sheet: -0.15 (0.16), residues: 1026 loop : -1.37 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 75 HIS 0.005 0.001 HIS I 112 PHE 0.011 0.001 PHE N 29 TYR 0.010 0.001 TYR E 11 ARG 0.004 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02585 ( 363) hydrogen bonds : angle 4.79056 ( 1026) SS BOND : bond 0.00041 ( 6) SS BOND : angle 0.27203 ( 12) covalent geometry : bond 0.00242 (20244) covalent geometry : angle 0.60291 (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 321 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 ILE cc_start: 0.9554 (mm) cc_final: 0.9337 (mm) REVERT: G 136 MET cc_start: 0.9092 (ppp) cc_final: 0.8875 (ppp) REVERT: g 66 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7753 (mtmm) REVERT: g 143 ASP cc_start: 0.8508 (t0) cc_final: 0.7995 (t0) REVERT: F 29 MET cc_start: 0.8029 (mmm) cc_final: 0.7630 (tpp) REVERT: A 58 TYR cc_start: 0.7133 (m-80) cc_final: 0.6796 (m-80) REVERT: A 69 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7443 (mt0) REVERT: B 72 MET cc_start: 0.8987 (tpp) cc_final: 0.8696 (tpt) REVERT: C 129 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7906 (mm-30) REVERT: C 134 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: D 101 LYS cc_start: 0.8568 (mppt) cc_final: 0.8346 (mmmt) REVERT: E 60 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7655 (p0) REVERT: H 72 MET cc_start: 0.7746 (mmm) cc_final: 0.6961 (mmm) REVERT: H 74 GLU cc_start: 0.8836 (pm20) cc_final: 0.7620 (pm20) REVERT: H 88 GLU cc_start: 0.8748 (tp30) cc_final: 0.8512 (tp30) REVERT: I 7 MET cc_start: 0.9006 (tpt) cc_final: 0.8630 (tpp) REVERT: I 41 GLU cc_start: 0.8232 (tt0) cc_final: 0.7673 (tm-30) REVERT: I 83 MET cc_start: 0.8806 (tmm) cc_final: 0.8494 (tmm) REVERT: J 3 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: J 51 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8975 (tttp) REVERT: J 60 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8039 (p0) REVERT: J 72 MET cc_start: 0.8883 (mmm) cc_final: 0.8316 (tpp) REVERT: J 150 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8804 (t0) REVERT: K 55 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8864 (mm-30) REVERT: K 78 GLU cc_start: 0.8681 (mp0) cc_final: 0.8241 (mp0) REVERT: K 88 GLU cc_start: 0.8414 (tp30) cc_final: 0.8156 (tp30) REVERT: K 128 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7859 (p90) REVERT: L 39 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: M 72 MET cc_start: 0.9514 (mmm) cc_final: 0.8749 (mmm) REVERT: N 55 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8709 (mm-30) REVERT: N 67 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8023 (p) REVERT: N 74 GLU cc_start: 0.8768 (pm20) cc_final: 0.8165 (pm20) REVERT: N 129 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: O 24 ASP cc_start: 0.8802 (m-30) cc_final: 0.8584 (p0) REVERT: P 11 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: P 145 MET cc_start: 0.8990 (ttp) cc_final: 0.8586 (mtp) outliers start: 64 outliers final: 31 residues processed: 291 average time/residue: 0.3151 time to fit residues: 151.2332 Evaluate side-chains 281 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 3.606 ------------------------------------------------------------------------------- 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 66 LYS 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 B residue 3 PHE Chi-restraints excluded: chain B residue 128 PHE 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 136 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 62 VAL 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 J residue 3 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 128 PHE Chi-restraints excluded: chain J residue 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 103 VAL Chi-restraints excluded: chain M residue 128 PHE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 128 PHE Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain P residue 11 TYR Chi-restraints excluded: chain P residue 128 PHE Chi-restraints excluded: chain Q residue 128 PHE Chi-restraints excluded: chain Q residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2598 > 50: distance: 80 - 84: 35.520 distance: 84 - 85: 37.523 distance: 85 - 86: 49.628 distance: 85 - 88: 68.880 distance: 86 - 87: 49.791 distance: 86 - 90: 38.977 distance: 88 - 89: 56.584 distance: 90 - 91: 27.940 distance: 90 - 96: 34.880 distance: 91 - 92: 38.517 distance: 91 - 94: 47.847 distance: 92 - 93: 52.627 distance: 92 - 97: 41.202 distance: 94 - 95: 10.039 distance: 95 - 96: 31.048 distance: 97 - 98: 39.732 distance: 98 - 99: 39.616 distance: 99 - 104: 52.864 distance: 101 - 102: 43.787 distance: 101 - 103: 39.281 distance: 104 - 105: 42.805 distance: 105 - 106: 24.956 distance: 105 - 108: 38.564 distance: 106 - 107: 35.883 distance: 106 - 110: 31.118 distance: 108 - 109: 18.622 distance: 110 - 111: 52.453 distance: 111 - 112: 12.019 distance: 111 - 114: 10.462 distance: 112 - 113: 38.665 distance: 112 - 117: 17.788 distance: 114 - 115: 35.922 distance: 114 - 116: 21.357 distance: 117 - 118: 22.725 distance: 118 - 119: 39.664 distance: 118 - 121: 31.012 distance: 119 - 120: 61.779 distance: 119 - 126: 41.195 distance: 121 - 122: 52.392 distance: 122 - 123: 49.930 distance: 123 - 124: 41.032 distance: 124 - 125: 33.371 distance: 126 - 127: 42.117 distance: 127 - 128: 47.330 distance: 127 - 130: 8.656 distance: 128 - 129: 17.252 distance: 128 - 134: 46.551 distance: 130 - 131: 63.335 distance: 130 - 132: 58.528 distance: 134 - 135: 43.718 distance: 135 - 136: 34.389 distance: 135 - 138: 16.495 distance: 136 - 137: 4.158 distance: 136 - 142: 40.401 distance: 138 - 139: 56.440 distance: 138 - 140: 44.223 distance: 139 - 141: 65.399 distance: 142 - 143: 26.772 distance: 143 - 144: 49.575 distance: 144 - 145: 35.423 distance: 144 - 150: 56.348 distance: 146 - 147: 26.349 distance: 147 - 148: 13.075 distance: 147 - 149: 27.612 distance: 150 - 151: 17.248 distance: 151 - 152: 47.535 distance: 151 - 154: 22.482 distance: 152 - 153: 43.793 distance: 152 - 159: 28.200 distance: 154 - 155: 22.861 distance: 155 - 156: 20.787 distance: 156 - 157: 3.662 distance: 156 - 158: 27.705