Starting phenix.real_space_refine on Sun May 18 14:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkj_9406/05_2025/5bkj_9406.cif" } resolution = 3.5 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= 0.004 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10692 2.51 5 N 2897 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16939 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 7.71, per 1000 atoms: 0.46 Number of scatterers: 16939 At special positions: 0 Unit cell: (150.7, 150.7, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3276 8.00 N 2897 7.00 C 10692 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 - 3.00 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: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 48.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.534A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.597A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.634A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.636A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.624A pdb=" N THR F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.770A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.572A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.973A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.618A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.663A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 325 through 334 removed outlier: 3.736A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN A 158 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.511A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN C 158 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN E 158 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.872A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN G 158 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.871A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2160 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: 5.20 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4581 1.33 - 1.45: 2559 1.45 - 1.57: 9908 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17168 Sorted by residual: bond pdb=" C01 YQ1 A 404 " pdb=" N01 YQ1 A 404 " ideal model delta sigma weight residual 1.524 1.468 0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.690 -0.054 2.00e-02 2.50e+03 7.40e+00 ... (remaining 17163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 22436 1.87 - 3.74: 585 3.74 - 5.61: 121 5.61 - 7.47: 40 7.47 - 9.34: 4 Bond angle restraints: 23186 Sorted by residual: angle pdb=" CG1 ILE D 285 " pdb=" CB ILE D 285 " pdb=" CG2 ILE D 285 " ideal model delta sigma weight residual 110.70 120.04 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CG1 ILE F 285 " pdb=" CB ILE F 285 " pdb=" CG2 ILE F 285 " ideal model delta sigma weight residual 110.70 120.00 -9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CG1 ILE H 285 " pdb=" CB ILE H 285 " pdb=" CG2 ILE H 285 " ideal model delta sigma weight residual 110.70 119.99 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CG1 ILE B 285 " pdb=" CB ILE B 285 " pdb=" CG2 ILE B 285 " ideal model delta sigma weight residual 110.70 119.96 -9.26 3.00e+00 1.11e-01 9.54e+00 angle pdb=" N LYS H 274 " pdb=" CA LYS H 274 " pdb=" C LYS H 274 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.47e+00 ... (remaining 23181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 9888 24.59 - 49.18: 524 49.18 - 73.77: 44 73.77 - 98.35: 28 98.35 - 122.94: 4 Dihedral angle restraints: 10488 sinusoidal: 4336 harmonic: 6152 Sorted by residual: dihedral pdb=" C01 PGW C 401 " pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " pdb=" O04 PGW C 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.94 -122.94 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW E 401 " pdb=" C19 PGW E 401 " pdb=" O03 PGW E 401 " pdb=" O04 PGW E 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.93 -122.93 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW A 401 " pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " pdb=" O04 PGW A 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.89 -122.89 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 2655 0.152 - 0.304: 29 0.304 - 0.455: 0 0.455 - 0.607: 0 0.607 - 0.759: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB ILE H 285 " pdb=" CA ILE H 285 " pdb=" CG1 ILE H 285 " pdb=" CG2 ILE H 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CB ILE D 285 " pdb=" CA ILE D 285 " pdb=" CG1 ILE D 285 " pdb=" CG2 ILE D 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 2685 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 252 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C VAL F 252 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 252 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN F 253 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 252 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C VAL B 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN B 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 252 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C VAL H 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL H 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN H 253 " 0.011 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5166 2.83 - 3.41: 16311 3.41 - 3.98: 30344 3.98 - 4.56: 41421 4.56 - 5.14: 65321 Nonbonded interactions: 158563 Sorted by model distance: nonbonded pdb=" NH1 ARG A 154 " pdb=" O HIS C 161 " model vdw 2.251 3.120 nonbonded pdb=" O HIS A 161 " pdb=" NH1 ARG G 154 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG C 154 " pdb=" O HIS E 161 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG E 154 " pdb=" O HIS G 161 " model vdw 2.283 3.120 nonbonded pdb=" O PHE A 75 " pdb=" OG1 THR A 78 " model vdw 2.304 3.040 ... (remaining 158558 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' and (resid 20 through 336 or resid 401)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 35.900 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 0.056 17168 Z= 0.264 Angle : 0.813 9.342 23186 Z= 0.452 Chirality : 0.061 0.759 2688 Planarity : 0.005 0.034 3000 Dihedral : 15.402 122.943 6536 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.09 % Allowed : 7.64 % Favored : 91.27 % 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: -3.93 (0.13), residues: 2140 helix: -2.86 (0.11), residues: 980 sheet: -0.60 (0.25), residues: 356 loop : -3.04 (0.16), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 123 HIS 0.004 0.001 HIS A 117 PHE 0.007 0.001 PHE C 40 TYR 0.015 0.002 TYR C 51 ARG 0.004 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.20029 ( 744) hydrogen bonds : angle 7.07524 ( 2160) covalent geometry : bond 0.00584 (17168) covalent geometry : angle 0.81314 (23186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 519 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8109 (m-80) cc_final: 0.7308 (m-80) REVERT: A 82 LEU cc_start: 0.9295 (mt) cc_final: 0.8800 (mp) REVERT: A 105 LYS cc_start: 0.8850 (tttt) cc_final: 0.8597 (tttm) REVERT: A 174 ASN cc_start: 0.8910 (t0) cc_final: 0.8412 (t0) REVERT: A 319 LEU cc_start: 0.9182 (tp) cc_final: 0.8978 (tp) REVERT: B 174 ASN cc_start: 0.8532 (m110) cc_final: 0.8323 (m-40) REVERT: B 310 TYR cc_start: 0.7881 (t80) cc_final: 0.7500 (t80) REVERT: B 316 ASP cc_start: 0.8070 (m-30) cc_final: 0.7837 (m-30) REVERT: D 310 TYR cc_start: 0.7899 (t80) cc_final: 0.7507 (t80) REVERT: D 333 TYR cc_start: 0.8638 (t80) cc_final: 0.8090 (t80) REVERT: F 310 TYR cc_start: 0.7710 (t80) cc_final: 0.7415 (t80) REVERT: F 333 TYR cc_start: 0.8559 (t80) cc_final: 0.8074 (t80) REVERT: H 310 TYR cc_start: 0.7671 (t80) cc_final: 0.7455 (t80) REVERT: H 333 TYR cc_start: 0.8557 (t80) cc_final: 0.8075 (t80) REVERT: C 82 LEU cc_start: 0.9220 (mt) cc_final: 0.8755 (mp) REVERT: C 102 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 105 LYS cc_start: 0.8836 (tttt) cc_final: 0.8599 (tttm) REVERT: C 174 ASN cc_start: 0.8920 (t0) cc_final: 0.8428 (t0) REVERT: C 305 ASP cc_start: 0.7778 (t0) cc_final: 0.7567 (t70) REVERT: E 33 TYR cc_start: 0.8685 (t80) cc_final: 0.8278 (t80) REVERT: E 96 GLU cc_start: 0.7580 (tt0) cc_final: 0.7356 (tt0) REVERT: E 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8565 (tttm) REVERT: E 174 ASN cc_start: 0.8898 (t0) cc_final: 0.8418 (t0) REVERT: E 270 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7537 (Cg_exo) REVERT: E 305 ASP cc_start: 0.7785 (t0) cc_final: 0.7531 (t70) REVERT: E 319 LEU cc_start: 0.9035 (tp) cc_final: 0.8831 (tp) REVERT: G 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8571 (tttm) REVERT: G 174 ASN cc_start: 0.8924 (t0) cc_final: 0.8420 (t0) outliers start: 20 outliers final: 0 residues processed: 527 average time/residue: 0.3295 time to fit residues: 245.6826 Evaluate side-chains 373 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 332 ASN D 286 HIS H 286 HIS H 332 ASN C 219 GLN E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119635 restraints weight = 21199.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122690 restraints weight = 13484.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124805 restraints weight = 9786.064| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17168 Z= 0.129 Angle : 0.500 5.269 23186 Z= 0.268 Chirality : 0.047 0.170 2688 Planarity : 0.003 0.044 3000 Dihedral : 9.181 74.975 2540 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.64 % Allowed : 13.65 % Favored : 84.72 % 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: -2.26 (0.16), residues: 2140 helix: -1.01 (0.15), residues: 992 sheet: -0.14 (0.26), residues: 356 loop : -2.71 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 123 HIS 0.008 0.001 HIS B 286 PHE 0.012 0.001 PHE F 251 TYR 0.018 0.001 TYR A 33 ARG 0.005 0.000 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 744) hydrogen bonds : angle 4.80841 ( 2160) covalent geometry : bond 0.00296 (17168) covalent geometry : angle 0.49977 (23186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 397 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8261 (m-80) cc_final: 0.7425 (m-80) REVERT: A 174 ASN cc_start: 0.8973 (t0) cc_final: 0.8410 (t0) REVERT: A 210 GLU cc_start: 0.7679 (tt0) cc_final: 0.7423 (tt0) REVERT: A 319 LEU cc_start: 0.9090 (tp) cc_final: 0.8868 (tp) REVERT: B 310 TYR cc_start: 0.8069 (t80) cc_final: 0.7840 (t80) REVERT: D 200 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8510 (tttt) REVERT: F 333 TYR cc_start: 0.8558 (t80) cc_final: 0.8196 (t80) REVERT: H 333 TYR cc_start: 0.8612 (t80) cc_final: 0.8185 (t80) REVERT: C 82 LEU cc_start: 0.9194 (mt) cc_final: 0.8784 (mp) REVERT: C 105 LYS cc_start: 0.8719 (tttt) cc_final: 0.8506 (tttm) REVERT: C 174 ASN cc_start: 0.8996 (t0) cc_final: 0.8453 (t0) REVERT: C 210 GLU cc_start: 0.7687 (tt0) cc_final: 0.7480 (tt0) REVERT: E 82 LEU cc_start: 0.9164 (mt) cc_final: 0.8788 (mp) REVERT: E 174 ASN cc_start: 0.8989 (t0) cc_final: 0.8440 (t0) REVERT: E 210 GLU cc_start: 0.7674 (tt0) cc_final: 0.7468 (tt0) REVERT: E 247 TYR cc_start: 0.8701 (m-80) cc_final: 0.8490 (m-80) REVERT: G 82 LEU cc_start: 0.9151 (mt) cc_final: 0.8791 (mp) REVERT: G 174 ASN cc_start: 0.8989 (t0) cc_final: 0.8436 (t0) REVERT: G 210 GLU cc_start: 0.7682 (tt0) cc_final: 0.7473 (tt0) outliers start: 30 outliers final: 18 residues processed: 414 average time/residue: 0.3126 time to fit residues: 186.3982 Evaluate side-chains 396 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 378 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 308 ARG Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 157 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN D 332 ASN F 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.144527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115258 restraints weight = 21313.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117438 restraints weight = 15599.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118574 restraints weight = 11442.070| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17168 Z= 0.114 Angle : 0.459 4.690 23186 Z= 0.244 Chirality : 0.046 0.145 2688 Planarity : 0.003 0.033 3000 Dihedral : 8.267 74.842 2540 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.57 % Allowed : 15.45 % Favored : 81.99 % 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: -1.43 (0.17), residues: 2140 helix: -0.14 (0.16), residues: 992 sheet: 0.17 (0.27), residues: 352 loop : -2.50 (0.17), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 123 HIS 0.008 0.001 HIS F 286 PHE 0.006 0.001 PHE H 140 TYR 0.022 0.001 TYR C 33 ARG 0.005 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 744) hydrogen bonds : angle 4.48264 ( 2160) covalent geometry : bond 0.00267 (17168) covalent geometry : angle 0.45853 (23186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8294 (m-80) cc_final: 0.7438 (m-80) REVERT: A 174 ASN cc_start: 0.8982 (t0) cc_final: 0.8361 (t0) REVERT: A 210 GLU cc_start: 0.7750 (tt0) cc_final: 0.7454 (tt0) REVERT: A 237 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7581 (mmt90) REVERT: B 200 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8477 (tttt) REVERT: B 333 TYR cc_start: 0.8638 (t80) cc_final: 0.8188 (t80) REVERT: D 200 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8512 (tttt) REVERT: D 333 TYR cc_start: 0.8655 (t80) cc_final: 0.8174 (t80) REVERT: F 333 TYR cc_start: 0.8636 (t80) cc_final: 0.8329 (t80) REVERT: H 333 TYR cc_start: 0.8590 (t80) cc_final: 0.8246 (t80) REVERT: C 65 TYR cc_start: 0.8364 (m-80) cc_final: 0.7539 (m-80) REVERT: C 82 LEU cc_start: 0.9203 (mt) cc_final: 0.8779 (mp) REVERT: C 102 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 105 LYS cc_start: 0.8783 (tttt) cc_final: 0.8566 (tttm) REVERT: C 174 ASN cc_start: 0.9019 (t0) cc_final: 0.8419 (t0) REVERT: C 210 GLU cc_start: 0.7747 (tt0) cc_final: 0.7511 (tt0) REVERT: E 82 LEU cc_start: 0.9196 (mt) cc_final: 0.8831 (mp) REVERT: E 104 MET cc_start: 0.8060 (mtt) cc_final: 0.7768 (ttp) REVERT: E 174 ASN cc_start: 0.9009 (t0) cc_final: 0.8356 (t0) REVERT: E 210 GLU cc_start: 0.7730 (tt0) cc_final: 0.7493 (tt0) REVERT: E 237 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7649 (mmt90) REVERT: E 247 TYR cc_start: 0.8748 (m-80) cc_final: 0.8454 (m-80) REVERT: G 82 LEU cc_start: 0.9191 (mt) cc_final: 0.8839 (mp) REVERT: G 102 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8204 (mm-30) REVERT: G 174 ASN cc_start: 0.9004 (t0) cc_final: 0.8384 (t0) REVERT: G 210 GLU cc_start: 0.7731 (tt0) cc_final: 0.7486 (tt0) REVERT: G 247 TYR cc_start: 0.8794 (m-80) cc_final: 0.8555 (m-80) REVERT: G 319 LEU cc_start: 0.9109 (tp) cc_final: 0.8872 (tp) outliers start: 47 outliers final: 38 residues processed: 406 average time/residue: 0.2953 time to fit residues: 175.9910 Evaluate side-chains 409 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 308 ARG Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 50.5551 > 50: distance: 28 - 133: 9.046 distance: 31 - 130: 4.726 distance: 46 - 121: 7.944 distance: 49 - 118: 4.079 distance: 93 - 113: 8.101 distance: 96 - 110: 5.084 distance: 105 - 110: 3.098 distance: 111 - 114: 3.146 distance: 112 - 113: 3.432 distance: 112 - 118: 4.253 distance: 115 - 116: 3.612 distance: 115 - 117: 7.237 distance: 118 - 119: 3.168 distance: 119 - 120: 6.695 distance: 120 - 121: 7.715 distance: 122 - 123: 5.575 distance: 123 - 124: 5.316 distance: 124 - 125: 3.721 distance: 124 - 130: 5.754 distance: 126 - 127: 3.396 distance: 126 - 128: 11.437 distance: 127 - 129: 9.437 distance: 130 - 131: 3.551 distance: 131 - 132: 5.205 distance: 132 - 134: 3.055 distance: 134 - 135: 6.078 distance: 135 - 136: 8.065 distance: 135 - 138: 12.901 distance: 136 - 137: 15.213 distance: 136 - 143: 23.919 distance: 138 - 139: 14.681 distance: 139 - 140: 9.943 distance: 140 - 141: 7.404 distance: 141 - 142: 21.639 distance: 143 - 149: 18.139 distance: 144 - 145: 11.870 distance: 144 - 147: 14.552 distance: 145 - 146: 12.121 distance: 145 - 150: 9.243 distance: 147 - 148: 8.930 distance: 148 - 149: 10.747 distance: 150 - 151: 5.253 distance: 151 - 152: 7.910 distance: 151 - 154: 4.325 distance: 152 - 159: 6.600 distance: 154 - 155: 12.787 distance: 155 - 156: 13.270 distance: 156 - 157: 11.610 distance: 156 - 158: 9.846 distance: 161 - 162: 3.508 distance: 161 - 168: 3.232 distance: 162 - 193: 10.189 distance: 163 - 164: 4.521 distance: 164 - 165: 3.111 distance: 165 - 167: 4.357 distance: 170 - 171: 3.369 distance: 170 - 176: 4.244 distance: 172 - 173: 4.231 distance: 172 - 174: 13.558 distance: 173 - 175: 6.317 distance: 176 - 177: 5.277 distance: 177 - 178: 3.847 distance: 177 - 180: 6.384 distance: 178 - 179: 3.452 distance: 178 - 185: 3.108 distance: 179 - 208: 4.898 distance: 180 - 181: 5.283 distance: 181 - 182: 11.326 distance: 182 - 183: 6.957 distance: 182 - 184: 5.905