Starting phenix.real_space_refine on Thu Aug 8 03:00:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/08_2024/7x1y_32952.cif" } resolution = 3.3 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= 0.003 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 P 36 5.49 5 Mg 12 5.21 5 S 84 5.16 5 C 13806 2.51 5 N 3852 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22032 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.13, per 1000 atoms: 0.55 Number of scatterers: 22032 At special positions: 0 Unit cell: (121.245, 119.875, 113.71, 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) S 84 16.00 P 36 15.00 Mg 12 11.99 O 4242 8.00 N 3852 7.00 C 13806 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.3 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 20 sheets defined 36.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 52 through 66 removed outlier: 4.055A pdb=" N SER A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.569A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.744A pdb=" N GLU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.687A pdb=" N MET A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.731A pdb=" N LEU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.740A pdb=" N MET A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 4.107A pdb=" N ALA A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.741A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'B' and resid 52 through 66 removed outlier: 4.059A pdb=" N SER B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.564A pdb=" N ILE B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.750A pdb=" N GLU B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 267 through 273 removed outlier: 3.552A pdb=" N MET B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.724A pdb=" N LEU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 321 through 332 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.703A pdb=" N MET B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.082A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.737A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'C' and resid 52 through 66 removed outlier: 4.074A pdb=" N SER C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.536A pdb=" N ILE C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.809A pdb=" N PHE C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.743A pdb=" N GLU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.550A pdb=" N MET C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.868A pdb=" N LEU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 321 through 332 Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.732A pdb=" N MET C 338 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.121A pdb=" N ALA C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.713A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'D' and resid 52 through 66 removed outlier: 4.055A pdb=" N SER D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.576A pdb=" N ILE D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.738A pdb=" N GLU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.769A pdb=" N MET D 273 " --> pdb=" O ARG D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.734A pdb=" N LEU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.742A pdb=" N MET D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.081A pdb=" N ALA D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 384 removed outlier: 3.745A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'E' and resid 52 through 66 removed outlier: 4.061A pdb=" N SER E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.564A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 159 through 175 removed outlier: 3.749A pdb=" N GLU E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 267 through 273 removed outlier: 3.552A pdb=" N MET E 273 " --> pdb=" O ARG E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 removed outlier: 3.771A pdb=" N LEU E 297 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 321 through 332 Processing helix chain 'E' and resid 334 through 341 removed outlier: 3.705A pdb=" N MET E 338 " --> pdb=" O ASP E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 4.084A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.761A pdb=" N LEU E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'F' and resid 52 through 66 removed outlier: 4.080A pdb=" N SER F 56 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 94 through 100 Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.533A pdb=" N ILE F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 159 through 175 removed outlier: 3.749A pdb=" N GLU F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 200 Processing helix chain 'F' and resid 267 through 273 removed outlier: 3.551A pdb=" N MET F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 removed outlier: 3.731A pdb=" N LEU F 297 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.744A pdb=" N MET F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 4.118A pdb=" N ALA F 354 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 384 removed outlier: 3.701A pdb=" N LEU F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 7.109A pdb=" N GLY A 71 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 106 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 73 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 346 removed outlier: 6.397A pdb=" N ILE A 284 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN A 414 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA A 286 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 283 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 438 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 285 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 440 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 287 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR A 442 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 441 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 7.124A pdb=" N GLY B 71 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 106 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE B 73 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.404A pdb=" N ILE B 284 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN B 414 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 286 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 283 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 438 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 285 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 440 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 287 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 442 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 4.329A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 471 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.103A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU C 43 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 207 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER C 45 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 13.013A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 344 through 346 removed outlier: 6.394A pdb=" N ILE C 284 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN C 414 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 286 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 283 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE C 438 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU C 285 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU C 440 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR C 287 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR C 442 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 441 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 107 removed outlier: 7.101A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 344 through 346 removed outlier: 6.404A pdb=" N ILE D 284 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN D 414 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 286 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 283 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE D 438 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 285 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 440 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 287 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR D 442 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 441 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB6, first strand: chain 'E' and resid 103 through 107 removed outlier: 7.125A pdb=" N GLY E 71 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU E 106 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE E 73 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 13.052A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 344 through 346 removed outlier: 6.401A pdb=" N ILE E 284 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN E 414 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA E 286 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 283 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE E 438 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 285 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU E 440 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 287 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR E 442 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 441 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 468 through 472 removed outlier: 4.310A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 471 " --> pdb=" O ASP E 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 107 removed outlier: 7.104A pdb=" N GLY F 71 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU F 106 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE F 73 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 13.011A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 344 through 346 removed outlier: 6.402A pdb=" N ILE F 284 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN F 414 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA F 286 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 283 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE F 438 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU F 285 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 440 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR F 287 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N TYR F 442 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 441 " --> pdb=" O ALA F 452 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2295 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: 6.84 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6820 1.34 - 1.45: 3350 1.45 - 1.57: 12016 1.57 - 1.69: 62 1.69 - 1.81: 150 Bond restraints: 22398 Sorted by residual: bond pdb=" CB PRO C 110 " pdb=" CG PRO C 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.77e+00 bond pdb=" CB PRO F 110 " pdb=" CG PRO F 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.73e+00 bond pdb=" CB PRO D 110 " pdb=" CG PRO D 110 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.86e+00 bond pdb=" CB PRO A 110 " pdb=" CG PRO A 110 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.58e+00 bond pdb=" CB PRO D 248 " pdb=" CG PRO D 248 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 ... (remaining 22393 not shown) Histogram of bond angle deviations from ideal: 95.34 - 104.22: 317 104.22 - 113.10: 12013 113.10 - 121.98: 13254 121.98 - 130.86: 4582 130.86 - 139.74: 98 Bond angle restraints: 30264 Sorted by residual: angle pdb=" CA PRO C 110 " pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 112.00 100.11 11.89 1.40e+00 5.10e-01 7.22e+01 angle pdb=" CA PRO F 110 " pdb=" N PRO F 110 " pdb=" CD PRO F 110 " ideal model delta sigma weight residual 112.00 100.14 11.86 1.40e+00 5.10e-01 7.18e+01 angle pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" CD PRO B 110 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.78e+01 angle pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" CD PRO E 110 " ideal model delta sigma weight residual 112.00 100.56 11.44 1.40e+00 5.10e-01 6.68e+01 angle pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" CD PRO A 248 " ideal model delta sigma weight residual 112.00 101.20 10.80 1.40e+00 5.10e-01 5.96e+01 ... (remaining 30259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 12142 18.02 - 36.04: 1112 36.04 - 54.06: 285 54.06 - 72.08: 93 72.08 - 90.10: 36 Dihedral angle restraints: 13668 sinusoidal: 5820 harmonic: 7848 Sorted by residual: dihedral pdb=" CA GLU E 319 " pdb=" C GLU E 319 " pdb=" N SER E 320 " pdb=" CA SER E 320 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU F 319 " pdb=" C GLU F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C ASP B 478 " pdb=" N ASP B 478 " pdb=" CA ASP B 478 " pdb=" CB ASP B 478 " ideal model delta harmonic sigma weight residual -122.60 -132.46 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 13665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2424 0.047 - 0.093: 680 0.093 - 0.140: 235 0.140 - 0.186: 33 0.186 - 0.233: 6 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" C PRO B 110 " pdb=" CB PRO B 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" C PRO E 110 " pdb=" CB PRO E 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP E 478 " pdb=" N ASP E 478 " pdb=" C ASP E 478 " pdb=" CB ASP E 478 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3375 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 478 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" CG ASP E 478 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP E 478 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP E 478 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 478 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" CG ASP B 478 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASP B 478 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP B 478 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 247 " 0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 248 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 248 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 248 " 0.047 5.00e-02 4.00e+02 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 4 2.01 - 2.74: 1675 2.74 - 3.46: 29160 3.46 - 4.18: 48850 4.18 - 4.90: 91873 Nonbonded interactions: 171562 Sorted by model distance: nonbonded pdb=" OE2 GLU D 318 " pdb=" OG SER D 379 " model vdw 1.293 3.040 nonbonded pdb=" OE2 GLU B 318 " pdb=" OG SER B 379 " model vdw 1.608 3.040 nonbonded pdb=" OE2 GLU C 318 " pdb=" OG SER C 379 " model vdw 1.671 3.040 nonbonded pdb=" OE2 GLU A 318 " pdb=" OG SER A 379 " model vdw 1.675 3.040 nonbonded pdb=" OG1 THR B 53 " pdb="MG MG B 904 " model vdw 2.037 2.170 ... (remaining 171557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.580 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 0.156 22398 Z= 0.416 Angle : 0.854 11.894 30264 Z= 0.492 Chirality : 0.050 0.233 3378 Planarity : 0.006 0.086 3858 Dihedral : 16.187 90.104 8628 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.48 % Favored : 91.30 % Rotamer: Outliers : 0.52 % Allowed : 0.82 % Favored : 98.66 % Cbeta Deviations : 0.08 % 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: -1.68 (0.15), residues: 2724 helix: -0.39 (0.17), residues: 876 sheet: -0.68 (0.20), residues: 672 loop : -1.88 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 92 HIS 0.006 0.002 HIS B 15 PHE 0.019 0.002 PHE C 237 TYR 0.019 0.002 TYR C 442 ARG 0.011 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 2.596 Fit side-chains revert: symmetry clash REVERT: C 321 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: D 321 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8277 (tpt-90) REVERT: E 321 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7871 (tpt-90) REVERT: F 321 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7820 (tpt-90) outliers start: 12 outliers final: 7 residues processed: 259 average time/residue: 0.4248 time to fit residues: 158.5513 Evaluate side-chains 200 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 321 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS C 463 HIS E 463 HIS F 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22398 Z= 0.452 Angle : 0.637 8.586 30264 Z= 0.340 Chirality : 0.045 0.144 3378 Planarity : 0.004 0.037 3858 Dihedral : 12.196 89.182 3469 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.31 % Favored : 92.47 % Rotamer: Outliers : 1.12 % Allowed : 7.92 % Favored : 90.96 % 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: -1.13 (0.16), residues: 2724 helix: 0.38 (0.18), residues: 906 sheet: -0.68 (0.20), residues: 678 loop : -1.66 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 92 HIS 0.005 0.001 HIS B 33 PHE 0.019 0.002 PHE E 237 TYR 0.020 0.001 TYR C 442 ARG 0.004 0.000 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 2.740 Fit side-chains outliers start: 26 outliers final: 25 residues processed: 222 average time/residue: 0.3831 time to fit residues: 127.7142 Evaluate side-chains 210 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22398 Z= 0.264 Angle : 0.531 7.047 30264 Z= 0.284 Chirality : 0.042 0.148 3378 Planarity : 0.003 0.036 3858 Dihedral : 10.454 88.956 3450 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.34 % Favored : 92.44 % Rotamer: Outliers : 1.21 % Allowed : 11.02 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2724 helix: 0.82 (0.18), residues: 912 sheet: -0.41 (0.20), residues: 666 loop : -1.56 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 92 HIS 0.003 0.001 HIS E 33 PHE 0.014 0.001 PHE E 237 TYR 0.014 0.001 TYR C 442 ARG 0.005 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 219 time to evaluate : 2.749 Fit side-chains outliers start: 28 outliers final: 22 residues processed: 232 average time/residue: 0.3733 time to fit residues: 130.9319 Evaluate side-chains 219 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 117 optimal weight: 0.0980 chunk 164 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1722 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: