Starting phenix.real_space_refine on Wed Mar 20 21:08:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/03_2024/8ekw_28214.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/03_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_28214/03_2024/8ekw_28214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/03_2024/8ekw_28214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/03_2024/8ekw_28214.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekw_28214/03_2024/8ekw_28214.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.87, per 1000 atoms: 0.54 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: 5.68 Conformation dependent library (CDL) restraints added in 2.3 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: 1.59 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: 3.82 Time building geometry restraints manager: 6.14 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 2.440 nonbonded pdb=" OD2 ASP C 179 " pdb=" OG SER C 185 " model vdw 2.216 2.440 nonbonded pdb=" NZ LYS B 80 " pdb=" O HOH B 301 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS H 80 " pdb=" O HOH H 301 " model vdw 2.244 2.520 nonbonded pdb=" NE ARG H 200 " pdb=" O LEU H 219 " model vdw 2.244 2.520 ... (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 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 7.750 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.110 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 62.230 ------------------------------------------------------------------------------- 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 : 1.747 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: 1.7772 time to fit residues: 591.7788 Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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: 4.9990 chunk 128 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 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: 0.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 142 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN D 217 ASN G 213 GLN I 217 ASN J 213 GLN J 217 ASN J 233 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14500 Z= 0.196 Angle : 0.509 4.891 19670 Z= 0.269 Chirality : 0.044 0.157 2190 Planarity : 0.005 0.063 2520 Dihedral : 4.385 58.727 1924 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.87 % Allowed : 9.48 % Favored : 88.65 % 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: 0.80 (0.21), residues: 1740 helix: 1.27 (0.23), residues: 540 sheet: 0.38 (0.21), residues: 460 loop : 0.23 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 88 HIS 0.003 0.001 HIS F 156 PHE 0.016 0.001 PHE J 114 TYR 0.019 0.002 TYR B 237 ARG 0.006 0.001 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 2 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 276 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 1.402 Fit side-chains REVERT: A 140 SER cc_start: 0.8232 (p) cc_final: 0.7960 (p) REVERT: B 97 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 102 LYS cc_start: 0.8969 (mttp) cc_final: 0.8766 (mtmm) REVERT: B 142 ASN cc_start: 0.8171 (t0) cc_final: 0.7749 (t0) REVERT: B 193 GLU cc_start: 0.7803 (mp0) cc_final: 0.7352 (mp0) REVERT: C 78 LYS cc_start: 0.8331 (mttp) cc_final: 0.8057 (mtmt) REVERT: C 95 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7597 (t0) REVERT: C 140 SER cc_start: 0.8227 (p) cc_final: 0.7952 (p) REVERT: D 164 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7245 (ttm170) REVERT: E 97 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: E 193 GLU cc_start: 0.7722 (mp0) cc_final: 0.7299 (mp0) REVERT: F 78 LYS cc_start: 0.8399 (mttp) cc_final: 0.8157 (mtpt) REVERT: F 142 ASN cc_start: 0.8296 (t0) cc_final: 0.7691 (t0) REVERT: F 200 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8231 (mtt180) REVERT: G 173 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6866 (mtm110) REVERT: H 173 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6865 (mtm110) REVERT: I 78 LYS cc_start: 0.8522 (mttp) cc_final: 0.8236 (mtpt) REVERT: I 166 GLN cc_start: 0.8275 (mt0) cc_final: 0.7939 (mp10) outliers start: 29 outliers final: 9 residues processed: 259 average time/residue: 1.8540 time to fit residues: 511.4779 Evaluate side-chains 237 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 194 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 217 ASN B 166 GLN D 166 GLN D 213 GLN D 217 ASN G 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14500 Z= 0.158 Angle : 0.467 4.673 19670 Z= 0.246 Chirality : 0.043 0.157 2190 Planarity : 0.004 0.058 2520 Dihedral : 3.904 42.980 1922 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.13 % Allowed : 12.19 % Favored : 85.68 % 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: 1.04 (0.21), residues: 1740 helix: 1.61 (0.22), residues: 540 sheet: 0.49 (0.21), residues: 460 loop : 0.27 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 159 HIS 0.002 0.000 HIS A 197 PHE 0.014 0.001 PHE G 114 TYR 0.020 0.002 TYR C 237 ARG 0.003 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 3 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 270 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8557 (mtp85) REVERT: A 213 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: B 97 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: B 102 LYS cc_start: 0.8930 (mttp) cc_final: 0.8706 (mtmm) REVERT: B 218 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: C 78 LYS cc_start: 0.8335 (mttp) cc_final: 0.8060 (mtmt) REVERT: C 140 SER cc_start: 0.8230 (p) cc_final: 0.7940 (p) REVERT: D 166 GLN cc_start: 0.8075 (mt0) cc_final: 0.7804 (mp10) REVERT: D 193 GLU cc_start: 0.7838 (mp0) cc_final: 0.7570 (mp0) REVERT: D 200 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (mtp85) REVERT: E 97 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: E 163 PRO cc_start: 0.8293 (Cg_endo) cc_final: 0.8080 (Cg_exo) REVERT: E 193 GLU cc_start: 0.7813 (mp0) cc_final: 0.7410 (mp0) REVERT: E 218 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: F 78 LYS cc_start: 0.8297 (mttp) cc_final: 0.8083 (mtpt) REVERT: F 142 ASN cc_start: 0.8173 (t0) cc_final: 0.7655 (t0) REVERT: F 193 GLU cc_start: 0.7775 (mp0) cc_final: 0.7205 (mp0) REVERT: G 173 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6852 (mtm110) REVERT: H 173 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6885 (mtm110) REVERT: I 78 LYS cc_start: 0.8399 (mttp) cc_final: 0.8140 (mtpt) REVERT: I 166 GLN cc_start: 0.8214 (mt0) cc_final: 0.7859 (mp10) REVERT: J 166 GLN cc_start: 0.8097 (mt0) cc_final: 0.7661 (mp10) REVERT: J 193 GLU cc_start: 0.7782 (mp0) cc_final: 0.7553 (mp0) outliers start: 33 outliers final: 12 residues processed: 249 average time/residue: 1.9789 time to fit residues: 523.5730 Evaluate side-chains 246 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 207 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.6806 > 50: distance: 34 - 164: 7.485 distance: 37 - 161: 9.498 distance: 48 - 145: 5.456 distance: 51 - 142: 12.755 distance: 62 - 133: 4.640 distance: 106 - 111: 12.209 distance: 111 - 112: 21.389 distance: 112 - 113: 32.540 distance: 112 - 115: 33.185 distance: 113 - 114: 41.103 distance: 113 - 119: 56.681 distance: 115 - 116: 35.123 distance: 116 - 117: 44.921 distance: 116 - 118: 25.281 distance: 119 - 120: 27.639 distance: 120 - 121: 12.344 distance: 120 - 123: 17.018 distance: 121 - 122: 12.297 distance: 121 - 130: 18.331 distance: 122 - 253: 8.160 distance: 123 - 124: 13.398 distance: 124 - 125: 9.415 distance: 125 - 126: 10.996 distance: 126 - 127: 4.438 distance: 127 - 129: 4.248 distance: 130 - 131: 18.138 distance: 131 - 132: 11.852 distance: 132 - 133: 10.244 distance: 132 - 134: 12.103 distance: 134 - 135: 3.353 distance: 134 - 242: 9.054 distance: 135 - 136: 7.208 distance: 135 - 138: 25.305 distance: 136 - 137: 6.836 distance: 136 - 142: 18.553 distance: 137 - 239: 16.235 distance: 138 - 139: 17.199 distance: 139 - 140: 20.188 distance: 139 - 141: 20.909 distance: 142 - 143: 10.470 distance: 143 - 144: 22.719 distance: 143 - 146: 24.019 distance: 144 - 145: 3.268 distance: 144 - 153: 13.373 distance: 146 - 147: 21.502 distance: 147 - 148: 9.030 distance: 147 - 149: 9.716 distance: 148 - 150: 4.150 distance: 150 - 152: 4.527 distance: 151 - 152: 4.607 distance: 153 - 154: 19.390 distance: 153 - 226: 8.077 distance: 154 - 155: 22.790 distance: 154 - 157: 13.060 distance: 155 - 156: 19.770 distance: 155 - 161: 15.373 distance: 157 - 158: 15.361 distance: 157 - 159: 8.497 distance: 158 - 160: 4.324 distance: 161 - 162: 8.078 distance: 162 - 163: 7.173 distance: 162 - 165: 3.335 distance: 163 - 164: 7.617 distance: 163 - 169: 6.909 distance: 165 - 166: 3.889 distance: 165 - 167: 4.916 distance: 166 - 168: 3.430 distance: 169 - 170: 7.658 distance: 171 - 177: 6.407 distance: 173 - 174: 6.313 distance: 174 - 175: 8.099 distance: 174 - 176: 5.778 distance: 177 - 178: 3.449 distance: 178 - 179: 11.096 distance: 178 - 181: 7.125 distance: 179 - 180: 8.535 distance: 179 - 185: 9.753 distance: 181 - 182: 4.101 distance: 182 - 183: 4.313 distance: 182 - 184: 3.252 distance: 185 - 186: 15.691 distance: 186 - 187: 10.644 distance: 186 - 189: 19.255 distance: 187 - 188: 21.001 distance: 187 - 194: 7.544 distance: 189 - 190: 4.795 distance: 190 - 191: 6.305 distance: 191 - 192: 3.351 distance: 192 - 193: 3.292