Starting phenix.real_space_refine on Fri Aug 9 10:20:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/08_2024/8ekw_28214.cif" } resolution = 2.83 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= 0.000 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14082 atoms to isotropic. 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 30 5.16 5 C 9120 2.51 5 N 2380 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 137": "OE1" <-> "OE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "I PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "J PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14552 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "C" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "F" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "G" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 8.20, per 1000 atoms: 0.56 Number of scatterers: 14552 At special positions: 0 Unit cell: (143.64, 140.4, 61.56, 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 30 16.00 O 3022 8.00 N 2380 7.00 C 9120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.96 Conformation dependent library (CDL) restraints added in 2.6 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 34.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.759A pdb=" N PHE A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'B' and resid 104 through 107 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'C' and resid 104 through 107 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.752A pdb=" N PHE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 152 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'E' and resid 104 through 107 Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.645A pdb=" N PHE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'G' and resid 104 through 107 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 134 through 140 removed outlier: 3.708A pdb=" N PHE G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 162 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 182 through 188 Processing helix chain 'G' and resid 224 through 241 Processing helix chain 'H' and resid 104 through 107 Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 134 through 140 removed outlier: 3.737A pdb=" N PHE H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 162 Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 224 through 241 Processing helix chain 'I' and resid 104 through 107 Processing helix chain 'I' and resid 125 through 134 Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.570A pdb=" N PHE I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 162 Processing helix chain 'I' and resid 182 through 188 Processing helix chain 'I' and resid 224 through 241 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 152 through 161 Processing helix chain 'J' and resid 163 through 167 Processing helix chain 'J' and resid 182 through 188 Processing helix chain 'J' and resid 224 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 4.702A pdb=" N THR A 91 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU A 177 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 147 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A 216 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 204 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 214 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 202 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 216 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 201 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL C 146 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 112 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS C 148 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE C 114 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU C 177 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 147 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 91 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102 removed outlier: 4.750A pdb=" N THR B 91 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 177 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 146 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 112 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N CYS B 148 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 114 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 201 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 200 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 213 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 204 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 202 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU D 216 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG D 200 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 146 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 112 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS D 148 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE D 114 " --> pdb=" O CYS D 148 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU D 177 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 147 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR D 91 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 97 through 102 removed outlier: 4.849A pdb=" N THR E 91 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU E 177 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA E 147 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL E 146 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL E 112 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS E 148 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE E 114 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY E 201 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG E 200 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN E 213 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE J 204 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE J 214 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU J 202 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU J 216 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG J 200 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL J 146 " --> pdb=" O TYR J 110 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL J 112 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS J 148 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE J 114 " --> pdb=" O CYS J 148 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LEU J 177 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA J 147 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR J 91 " --> pdb=" O SER J 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 97 through 102 removed outlier: 4.782A pdb=" N THR F 91 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU F 177 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA F 147 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL F 146 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL F 112 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N CYS F 148 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 114 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY F 201 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG F 200 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU F 216 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 202 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 214 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 204 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 213 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG G 200 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY G 201 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR G 110 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL G 146 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL G 112 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N CYS G 148 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE G 114 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU G 177 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA G 147 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR G 91 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 97 through 102 removed outlier: 4.832A pdb=" N THR H 91 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU H 177 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA H 147 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR H 110 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL H 146 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL H 112 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS H 148 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE H 114 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY H 201 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG H 200 " --> pdb=" O ASN H 217 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 213 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I 213 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG I 200 " --> pdb=" O ASN I 217 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY I 201 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR I 110 " --> pdb=" O GLU I 144 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL I 146 " --> pdb=" O TYR I 110 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL I 112 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS I 148 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE I 114 " --> pdb=" O CYS I 148 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU I 177 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I 147 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR I 91 " --> pdb=" O SER I 178 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1461 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: 4.07 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2352 1.31 - 1.43: 3974 1.43 - 1.56: 8143 1.56 - 1.68: 1 1.68 - 1.81: 30 Bond restraints: 14500 Sorted by residual: bond pdb=" CA PRO C 220 " pdb=" C PRO C 220 " ideal model delta sigma weight residual 1.516 1.431 0.085 1.42e-02 4.96e+03 3.57e+01 bond pdb=" CA ASP C 218 " pdb=" C ASP C 218 " ideal model delta sigma weight residual 1.528 1.450 0.078 1.33e-02 5.65e+03 3.40e+01 bond pdb=" CA PRO D 220 " pdb=" C PRO D 220 " ideal model delta sigma weight residual 1.516 1.429 0.087 1.61e-02 3.86e+03 2.93e+01 bond pdb=" CA SER E 178 " pdb=" CB SER E 178 " ideal model delta sigma weight residual 1.531 1.453 0.077 1.52e-02 4.33e+03 2.60e+01 bond pdb=" CA ASP D 218 " pdb=" C ASP D 218 " ideal model delta sigma weight residual 1.528 1.460 0.068 1.37e-02 5.33e+03 2.44e+01 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.46: 523 107.46 - 114.10: 8156 114.10 - 120.75: 6017 120.75 - 127.40: 4815 127.40 - 134.04: 159 Bond angle restraints: 19670 Sorted by residual: angle pdb=" N ASP D 218 " pdb=" CA ASP D 218 " pdb=" C ASP D 218 " ideal model delta sigma weight residual 110.53 100.81 9.72 1.29e+00 6.01e-01 5.68e+01 angle pdb=" N LEU D 219 " pdb=" CA LEU D 219 " pdb=" C LEU D 219 " ideal model delta sigma weight residual 113.16 122.09 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" C PRO D 220 " pdb=" CA PRO D 220 " pdb=" CB PRO D 220 " ideal model delta sigma weight residual 112.21 103.94 8.27 1.56e+00 4.11e-01 2.81e+01 angle pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" C VAL C 221 " ideal model delta sigma weight residual 109.21 116.15 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N LEU C 219 " pdb=" CA LEU C 219 " pdb=" C LEU C 219 " ideal model delta sigma weight residual 113.16 120.38 -7.22 1.42e+00 4.96e-01 2.58e+01 ... (remaining 19665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7694 17.45 - 34.91: 697 34.91 - 52.36: 121 52.36 - 69.82: 13 69.82 - 87.27: 15 Dihedral angle restraints: 8540 sinusoidal: 3460 harmonic: 5080 Sorted by residual: dihedral pdb=" C VAL C 221 " pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" CB VAL C 221 " ideal model delta harmonic sigma weight residual -122.00 -134.72 12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CA ARG A 223 " pdb=" CB ARG A 223 " ideal model delta harmonic sigma weight residual 122.80 133.58 -10.78 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" N LEU D 219 " pdb=" C LEU D 219 " pdb=" CA LEU D 219 " pdb=" CB LEU D 219 " ideal model delta harmonic sigma weight residual 122.80 133.43 -10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2135 0.123 - 0.245: 50 0.245 - 0.368: 1 0.368 - 0.490: 0 0.490 - 0.613: 4 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA LEU C 219 " pdb=" N LEU C 219 " pdb=" C LEU C 219 " pdb=" CB LEU C 219 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" CA LEU D 219 " pdb=" N LEU D 219 " pdb=" C LEU D 219 " pdb=" CB LEU D 219 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA VAL C 221 " pdb=" N VAL C 221 " pdb=" C VAL C 221 " pdb=" CB VAL C 221 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 2187 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 218 " -0.016 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C ASP C 218 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP C 218 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 219 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 162 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO G 163 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 163 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 163 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 218 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ASP D 218 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP D 218 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 219 " -0.014 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1838 2.75 - 3.28: 13540 3.28 - 3.82: 24618 3.82 - 4.36: 32206 4.36 - 4.90: 53262 Nonbonded interactions: 125464 Sorted by model distance: nonbonded pdb=" OD2 ASP F 179 " pdb=" OG SER F 185 " model vdw 2.207 3.040 nonbonded pdb=" OD2 ASP C 179 " pdb=" OG SER C 185 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS B 80 " pdb=" O HOH B 301 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS H 80 " pdb=" O HOH H 301 " model vdw 2.244 3.120 nonbonded pdb=" NE ARG H 200 " pdb=" O LEU H 219 " model vdw 2.244 3.120 ... (remaining 125459 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.660 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.006 0.087 14500 Z= 0.388 Angle : 0.659 16.290 19670 Z= 0.360 Chirality : 0.054 0.613 2190 Planarity : 0.006 0.082 2520 Dihedral : 13.689 87.275 5280 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.26 % Allowed : 0.32 % Favored : 99.42 % Cbeta Deviations : 0.18 % 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: 0.13 (0.20), residues: 1740 helix: 0.54 (0.23), residues: 550 sheet: -0.26 (0.22), residues: 450 loop : 0.17 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 88 HIS 0.003 0.001 HIS F 197 PHE 0.019 0.002 PHE D 115 TYR 0.009 0.002 TYR B 110 ARG 0.012 0.001 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 311 time to evaluate : 1.713 Fit side-chains REVERT: A 140 SER cc_start: 0.8106 (p) cc_final: 0.7824 (p) REVERT: B 142 ASN cc_start: 0.8187 (t0) cc_final: 0.7844 (t0) REVERT: B 151 ASP cc_start: 0.8923 (m-30) cc_final: 0.8694 (m-30) REVERT: B 206 ASP cc_start: 0.8353 (p0) cc_final: 0.8130 (p0) REVERT: C 78 LYS cc_start: 0.8226 (mttp) cc_final: 0.8026 (mtmt) REVERT: C 140 SER cc_start: 0.8190 (p) cc_final: 0.7901 (p) REVERT: C 206 ASP cc_start: 0.8278 (p0) cc_final: 0.8035 (p0) REVERT: D 218 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: E 151 ASP cc_start: 0.8958 (m-30) cc_final: 0.8729 (m-30) REVERT: E 179 ASP cc_start: 0.8690 (t0) cc_final: 0.8404 (t0) REVERT: E 206 ASP cc_start: 0.8244 (p0) cc_final: 0.7922 (p0) REVERT: F 78 LYS cc_start: 0.8451 (mttp) cc_final: 0.8132 (mtpt) REVERT: F 99 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8200 (mmtp) REVERT: F 142 ASN cc_start: 0.8381 (t0) cc_final: 0.7902 (t0) REVERT: G 142 ASN cc_start: 0.8338 (t0) cc_final: 0.7767 (t0) REVERT: H 142 ASN cc_start: 0.8202 (t0) cc_final: 0.7596 (t0) REVERT: H 179 ASP cc_start: 0.8727 (t0) cc_final: 0.8426 (t0) REVERT: I 78 LYS cc_start: 0.8398 (mttp) cc_final: 0.8190 (mtpt) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 1.6389 time to fit residues: 546.0391 Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain J residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: